The following extracts from the file 6rxn.ins (provided together with 6rxn.hkl as an example) illustrate a number of points. The structure was determined by Stenkamp, Sieker & Jensen, (1990) who have kindly given permission for it to be used in this way. As usual in .ins files, comments may be included as REM instructions or after exclamation marks. The resolution of 1.5Å does not quite justify refinement of all non-hydrogen atoms anisotropically ('ANIS' before the first atom would specify this), but the iron and sulfur atoms should be made anisotropic as shown below. Note that it would be better to flag the Rfree reflections randomly using SHELXPRO rather than just using every twelth reflection.
TITL Rubredoxin in P1 (from 6RXN in PDB)
CELL 1.54178 24.920 17.790 19.720 101.00 83.40 104.50 ! Lambda & cell
ZERR 1 0.025 0.018 0.020 0.05 0.05 0.05 ! Z & cell esds
LATT -1 ! Space group P1
SFAC C H N O S FE ! Scattering factor types and
UNIT 224 498 55 136 6 1 ! unit-cell contents
DEFS 0.02 0.2 0.01 0.05 ! Global default restraint esds
CGLS 10 -12 ! 10 Conjugate gradient cycles, every 12th reflection
SHEL 999 0.1 ! for R(free), all other data used for refinement
FMAP 2 ! Difference Fourier
PLAN 200 2.3 ! Peaksearch and identification of potential waters
LIST 6 ! Output phased reflection file to generate maps etc.
WPDB ! Write PDB output file
HTAB ! Output analysis of hydrogen bonds (requires H-atoms !)
DELU $C_* $N_* $O_* $S_* ! Rigid bond retraints - ignored for iso.
SIMU 0.1 $C_* $N_* $O_* $S_* ! Similar U restraints - iso. or anis.
! Esd should be changed to ca. 0.05 if whole structure is anis.
ISOR 0.1 O_201 > LAST ! Approximate isotropic restraints for waters;
! ignored for isotropic
ANIS_* FE SD SG ! Make iron and all sulfur atoms anisotropic
CONN 0 O_201 > LAST ! Don't include water in connectivity array and
BUMP ! generate antibumping restraints automatically
SWAT ! Diffuse water model
REM HOPE ! Anisotropic scaling not included
MERG 4 ! Remove MERG 4 if Friedel opposites should not be merged
MORE 1 ! MORE 0 for minimum, 2 or 3 for more output for diagnostics
REM Special restraints etc. specific to this structure follow:
REM HFIX 43 C1_1 !
DFIX C1_1 N_1 1.329 ! O=C(H)- (formyl) on N-terminus
DFIX C1_1 O1_1 1.231 ! incorporated into residue 1
DANG N_1 O1_1 2.250 !
DANG C1_1 CA_1 2.435 !
DFIX_52 C OT1 C OT2 1.249 !
DANG_52 CA OT1 CA OT2 2.379 ! Ionized carboxyl at C-terminus
DANG_52 OT1 OT2 2.194 !
SADI_54 0.04 FE SG_6 FE SG_9 FE SG_39 FE SG_42 ! Equal but unknown Fe-S
SADI_54 0.08 FE CB_6 FE CB_9 FE CB_39 FE CB_42 ! distances around Fe
REM HFIX 83 SG_38 SG_138 ! -SH for remaining cysteine (disordered)
DFIX C_18 N_26 1.329 ! Patch break in numbering - residues
DANG O_18 N_26 2.250 ! 18 and 26 are bonded but there is a
DANG CA_18 N_26 2.425 ! gap in numbering for compatibility
DANG C_18 CA_26 2.435 ! with other rubredoxins that have an
FLAT 0.3 O_18 CA_18 N_26 C_18 CA_26 ! extra loop
RTAB Omeg CA_18 C_18 N_26 CA_26 !
RTAB Phi C_18 N_26 CA_26 C_26 !
RTAB Psi N_18 CA_18 C_18 N_26 !
REM DFIX from CSD and R.A.Engh & R.Huber, Acta Cryst. A47 (1991) 392.
REM Remove 'REM ' before HFIX to activate H-atom generation
REM HFIX_ALA 43 N
REM HFIX_ALA 13 CA
REM HFIX_ALA 33 CB
REM HFIX_ASN 43 N
REM HFIX_ASN 13 CA
REM HFIX_ASN 23 CB
REM HFIX_ASN 93 ND2
REM HFIX_ASP 43 N
REM HFIX_ASP 13 CA
REM HFIX_ASP 23 CB
... etc ...
REM HFIX_VAL 43 N
REM HFIX_VAL 13 CA CB
REM HFIX_VAL 33 CG1 CG2
REM Peptide standard torsion angles and restraints
RTAB_* Omeg CA C N_+ CA_+
RTAB_* Phi C_- N CA C
RTAB_* Psi N CA C N_+
RTAB_* Cvol CA
DFIX_* 1.329 C_- N
DANG_* 2.425 CA_- N
DANG_* 2.250 O_- N
DANG_* 2.435 C_- CA
FLAT_* 0.3 O_- CA_- N C_- CA
REM Standard amino-acid restraints etc.
CHIV_ALA C
CHIV_ALA 2.477 CA
DFIX_ALA 1.231 C O
DFIX_ALA 1.525 C CA
DFIX_ALA 1.521 CA CB
DFIX_ALA 1.458 N CA
DANG_ALA 2.462 C N
DANG_ALA 2.401 O CA
DANG_ALA 2.503 C CB
DANG_ALA 2.446 CB N
RTAB_ASN Chi N CA CB CG
CHIV_ASN C CG
CHIV_ASN 2.503 CA
DFIX_ASN 1.231 C O CG OD1
DFIX_ASN 1.525 C CA
DFIX_ASN 1.458 N CA
DFIX_ASN 1.530 CA CB
DFIX_ASN 1.516 CB CG
DFIX_ASN 1.328 CG ND2
DANG_ASN 2.401 O CA
DANG_ASN 2.462 C N
DANG_ASN 2.455 CB N
DANG_ASN 2.504 C CB
DANG_ASN 2.534 CA CG
DANG_ASN 2.393 CB OD1
DANG_ASN 2.419 CB ND2
DANG_ASN 2.245 OD1 ND2
RTAB_ASP Chi N CA CB CG
CHIV_ASP C CG
CHIV_ASP 2.503 CA
DFIX_ASP 1.231 C O
DFIX_ASP 1.525 C CA
DFIX_ASP 1.530 CA CB
DFIX_ASP 1.516 CB CG
DFIX_ASP 1.458 CA N
DFIX_ASP 1.249 CG OD1 CG OD2
DANG_ASP 2.401 O CA
DANG_ASP 2.462 C N
DANG_ASP 2.455 CB N
DANG_ASP 2.504 C CB
DANG_ASP 2.534 CA CG
DANG_ASP 2.379 CB OD1 CB OD2
DANG_ASP 2.194 OD1 OD2
RTAB_CYS Chi N CA CB SG
CHIV_CYS C
CHIV_CYS 2.503 CA
DFIX_CYS 1.231 C O
DFIX_CYS 1.525 C CA
DFIX_CYS 1.458 N CA
DFIX_CYS 1.530 CA CB
DFIX_CYS 1.808 CB SG
DANG_CYS 2.401 O CA
DANG_CYS 2.504 C CB
DANG_CYS 2.455 CB N
DANG_CYS 2.462 C N
DANG_CYS 2.810 CA SG
... etc ...
RTAB_VAL Chi N CA CB CG1
RTAB_VAL Chi N CA CB CG2
CHIV_VAL C
CHIV_VAL 2.516 CA
DFIX_VAL 1.231 C O
DFIX_VAL 1.458 N CA
DFIX_VAL 1.525 C CA
DFIX_VAL 1.540 CA CB
DFIX_VAL 1.521 CB CG2 CB CG1
DANG_VAL 2.401 O CA
DANG_VAL 2.462 C N
DANG_VAL 2.497 C CB
DANG_VAL 2.515 CA CG1 CA CG2
DANG_VAL 2.479 N CB
DANG_VAL 2.504 CG1 CG2
WGHT 0.100000
FVAR 1.00000 0.5 0.5 0.5 0.5
RESI 1 MET
C1 1 -0.01633 0.35547 0.44703 11.00000 0.11817
O1 4 0.01012 0.32681 0.48491 11.00000 0.17896
N 3 0.00712 0.35446 0.37983 11.00000 0.11863
CA 1 0.05947 0.33273 0.35391 11.00000 0.06229
CB 1 0.07411 0.33732 0.27909 11.00000 0.15678
CG 1 0.03196 0.28864 0.22872 11.00000 0.14569
SD 5 0.04907 0.31846 0.14359 11.00000 0.23570
CE 1 0.11380 0.29170 0.12261 11.00000 0.21476
C 1 0.10634 0.38738 0.39766 11.00000 0.09178
O 4 0.10329 0.45513 0.41972 11.00000 0.16480
RESI 2 GLN
N 3 0.14741 0.35678 0.40741 11.00000 0.08599
CA 1 0.18940 0.39931 0.45565 11.00000 0.09291
CB 1 0.22933 0.34643 0.45886 11.00000 0.13253
CG 1 0.27354 0.38674 0.51173 11.00000 0.09866
CD 1 0.24547 0.38838 0.58387 11.00000 0.05748
OE1 4 0.22482 0.32772 0.60689 11.00000 0.16301
NE2 3 0.24704 0.46053 0.62045 11.00000 0.10164
C 1 0.22198 0.47895 0.43826 11.00000 0.08193
O 4 0.25019 0.48377 0.38408 11.00000 0.10402
RESI 3 LYS
N 3 0.21781 0.54034 0.48673 11.00000 0.07413
CA 1 0.25088 0.62006 0.47934 11.00000 0.05181
CB 1 0.21991 0.68311 0.51795 11.00000 0.09646
CG 1 0.16130 0.66288 0.49255 11.00000 0.10455
CD 1 0.12843 0.72146 0.52924 11.00000 0.22324
CE 1 0.10532 0.70085 0.60053 11.00000 0.26354
NZ 3 0.05943 0.74195 0.62796 11.00000 0.40338
C 1 0.30678 0.63497 0.50917 11.00000 0.05714
O 4 0.31462 0.59598 0.55179 11.00000 0.07986
... etc ...
RESI 12 GLU
N 3 0.41413 1.09215 0.48246 11.00000 0.06790
CA 1 0.37955 1.01183 0.48195 11.00000 0.05761
PART 1
CB 1 0.32666 1.01321 0.52971 21.00000 0.12219
CG 1 0.29679 0.93111 0.54638 21.00000 0.15333
CD 1 0.25357 0.93709 0.60700 21.00000 0.20272
OE1 4 0.24346 1.00278 0.63210 21.00000 0.26315
OE2 4 0.23012 0.87537 0.63031 21.00000 0.21375
PART 2
CB 1 0.32549 1.01718 0.52772 -21.00000 0.12065
CG 1 0.27756 0.94582 0.50954 -21.00000 0.15928
CD 1 0.22547 0.95184 0.55635 -21.00000 0.20457
OE1 4 0.20774 0.90241 0.59575 -21.00000 0.22329
OE2 4 0.20259 1.00588 0.55325 -21.00000 0.31441
PART 0
C 1 0.36477 0.97439 0.40859 11.00000 0.04768
O 4 0.34317 1.00861 0.37369 11.00000 0.06890
... etc ...
RESI 38 CYS
N 3 0.77141 0.92674 0.00625 11.00000 0.10936
CA 1 0.78873 0.97402 0.07449 11.00000 0.13706
PART 1
CB 1 0.83868 1.04271 0.05517 41.00000 0.11889
SG 5 0.89948 1.00271 0.02305 41.00000 0.18205
PART 2
CB 1 0.84149 1.03666 0.06538 -41.00000 0.14933
SG 5 0.83686 1.10360 0.01026 -41.00000 0.17328
PART 0
C 1 0.74143 1.01670 0.10383 11.00000 0.08401
O 4 0.70724 1.02319 0.06903 11.00000 0.10188
RESI 39 CYS
N 3 0.74699 1.04547 0.17051 11.00000 0.08888
CA 1 0.70682 1.09027 0.20876 11.00000 0.06869
CB 1 0.72588 1.11964 0.28230 11.00000 0.04269
SG 5 0.67932 1.17560 0.33481 11.00000 0.08016
C 1 0.70922 1.16093 0.17333 11.00000 0.06208
O 4 0.75427 1.20325 0.15858 11.00000 0.07437
... etc ...
RESI 52 ALA
N 3 0.33596 0.63469 0.69557 11.00000 0.04662
CA 1 0.30961 0.68882 0.74487 11.00000 0.08939
CB 1 0.34040 0.77357 0.74194 11.00000 0.13277
C 1 0.24852 0.67507 0.73435 11.00000 0.09032
OT1 4 0.22236 0.72170 0.77321 11.00000 0.11368
OT2 4 0.22682 0.61667 0.69191 11.00000 0.08341
RESI 54 FE
FE 6 0.72017 1.22290 0.43784 11.00000 0.07929
REM Only the waters with high occupancies and low U's have been
REM retained, and all the occupancies have been reset to 1, with
REM a view to running the automatic water divining. Water
REM residue numbers have been changed to start at 201.
RESI 201 HOH
O 4 0.13450 0.53192 0.60802 11.00000 0.13132
RESI 202 HOH
O 4 0.84795 0.53873 0.69488 11.00000 0.15273
RESI 203 HOH
O 4 0.27771 0.95750 0.25086 11.00000 0.11315
RESI 204 HOH
O 4 0.37066 0.71872 0.90376 11.00000 0.10854
... etc ...
RESI 233 HOH
O 4 0.27813 1.38725 0.25914 11.00000 0.10698
HKLF 3
END