Resolution: 1.5→28.87 Å / Num. obs: 17165 / % possible obs: 98.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 4.9
Reflection shell
Diffraction-ID: 1
Resolution (Å)
% possible obs (%)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Rsym value
1.63-1.67
87.7
2.5
0.551
1.4
1098
0.551
1.67-1.72
94
2.9
0.465
1.6
1147
0.465
1.72-1.77
99.7
3.5
0.354
2.2
1204
0.354
1.77-1.82
100
3.7
0.31
2.4
1180
0.31
1.82-1.88
100
3.6
0.223
3.4
1137
0.223
1.88-1.95
100
3.6
0.163
4.4
1093
0.163
1.95-2.02
100
3.6
0.122
5.8
1063
0.122
2.02-2.1
100
3.7
0.1
6.9
1026
0.1
2.1-2.2
100
3.6
0.081
8.8
977
0.081
2.2-2.31
100
3.6
0.078
8.5
954
0.078
2.31-2.43
100
3.6
0.07
9.6
891
0.07
2.43-2.58
100
3.6
0.059
11.4
860
0.059
2.58-2.76
100
3.6
0.056
11.4
800
0.056
2.76-2.98
100
3.6
0.056
11.1
757
0.056
2.98-3.26
100
3.6
0.054
11.3
712
0.054
3.26-3.64
100
3.6
0.039
15.1
628
0.039
3.64-4.21
99.9
3.5
0.038
16
559
0.038
4.21-5.15
99.5
3.5
0.037
16.7
477
0.037
5.15-7.29
99.4
3.4
0.041
14.1
380
0.041
7.29-28.87
96.4
3.1
0.062
4.6
222
0.062
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0005
refinement
SCALA
datascaling
PDB_EXTRACT
1.601
dataextraction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
SOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.63→28.87 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.553 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.096 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.NO DENSITY OBSERVED FOR RESIDUES 119-147. 3.EXTRA DENSITY OBSERVED BETWEEN RESIDUES 87-92 HAS BEEN MODELED UNKNOWN LIGAND. HOMOLOGY ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.NO DENSITY OBSERVED FOR RESIDUES 119-147. 3.EXTRA DENSITY OBSERVED BETWEEN RESIDUES 87-92 HAS BEEN MODELED UNKNOWN LIGAND. HOMOLOGY SEARCHES INDICATE THAT THIS IS A PUTA COENZYME-A BINDING SITE. 4.ONE SULPHATE GROUP WAS FOUND IN THE MODEL DURING THE REFINEMEN FROMTHE CRYSTALLIZATION CONDITION WITH MGSO4.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.217
830
4.8 %
RANDOM
Rwork
0.181
-
-
-
all
0.183
-
-
-
obs
-
16334
98.42 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 28.222 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.57 Å2
0 Å2
0 Å2
2-
-
0.06 Å2
0 Å2
3-
-
-
-1.64 Å2
Refinement step
Cycle: LAST / Resolution: 1.63→28.87 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
980
0
15
122
1117
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
1047
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
928
X-RAY DIFFRACTION
r_angle_refined_deg
1.586
1.931
1423
X-RAY DIFFRACTION
r_angle_other_deg
1.215
3
2170
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.383
5
130
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
43.896
24.615
52
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.472
15
198
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.146
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.086
0.2
157
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1165
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
210
X-RAY DIFFRACTION
r_nbd_refined
0.304
0.2
236
X-RAY DIFFRACTION
r_nbd_other
0.185
0.2
960
X-RAY DIFFRACTION
r_nbtor_refined
0.18
0.2
513
X-RAY DIFFRACTION
r_nbtor_other
0.085
0.2
597
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.17
0.2
97
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.218
0.2
13
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.276
0.2
46
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.167
0.2
13
X-RAY DIFFRACTION
r_mcbond_it
2.142
3
649
X-RAY DIFFRACTION
r_mcbond_other
0.51
3
253
X-RAY DIFFRACTION
r_mcangle_it
2.909
5
1015
X-RAY DIFFRACTION
r_scbond_it
5.513
8
465
X-RAY DIFFRACTION
r_scangle_it
7.261
11
404
LS refinement shell
Resolution: 1.63→1.672 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.299
61
-
Rwork
0.289
1034
-
obs
-
-
87.04 %
Refinement TLS params.
Method: refined / Origin x: 4.6567 Å / Origin y: 14.3597 Å / Origin z: 13.9026 Å
11
12
13
21
22
23
31
32
33
T
-0.1576 Å2
0.0118 Å2
-0.0151 Å2
-
-0.1367 Å2
-0.0245 Å2
-
-
-0.1562 Å2
L
0.9834 °2
0.18 °2
0.63 °2
-
2.1993 °2
-1.2433 °2
-
-
3.5469 °2
S
0.0458 Å °
-0.0647 Å °
-0.0372 Å °
-0.1223 Å °
-0.0102 Å °
0.0537 Å °
0.0233 Å °
-0.0237 Å °
-0.0356 Å °
+
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