SEQUENCE THE CLOSEST SEQUENCE MATCH FOR THIS ENTRY IS AN UNIPROT ENTRY A6Y463_VIBCH, OF THE VIBRIO ... SEQUENCE THE CLOSEST SEQUENCE MATCH FOR THIS ENTRY IS AN UNIPROT ENTRY A6Y463_VIBCH, OF THE VIBRIO CHOLERAE RC385 STRAIN. AUTHORS STATE THAT THE SOURCE OF THEIR PROTEIN IS VIBRIO CHOLERAE O1 BIOVAR ELTOR STRAIN N16961, NCBI ACCESSION AAF94064, GI:9655358.
Resolution: 1.53→1.58 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 12259 / Rsym value: 0.359 / % possible all: 76.5
-
Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
SBC-Collect
datacollection
HKL-3000
datacollection
HKL-3000
datareduction
HKL-3000
datascaling
HKL-3000
phasing
SHELX
phasing
MLPHARE
phasing
RESOLVE
phasing
ARP/wARP
modelbuilding
Refinement
Method to determine structure: SAD / Resolution: 1.53→26.16 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.773 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.079 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: Program PHENIX has also been used in refinement
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.183
7527
5 %
RANDOM
Rwork
0.143
-
-
-
all
0.145
142270
-
-
obs
0.145
142270
93.89 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 21.199 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.62 Å2
-0.18 Å2
-0.29 Å2
2-
-
0.89 Å2
1.12 Å2
3-
-
-
0.57 Å2
Refinement step
Cycle: LAST / Resolution: 1.53→26.16 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
8197
0
94
1177
9468
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.021
9589
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.578
1.948
13200
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.13
5
1238
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
40.448
24.981
526
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.391
15
1604
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
11.071
15
65
X-RAY DIFFRACTION
r_chiral_restr
0.112
0.2
1377
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
7849
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.233
0.2
4890
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.307
0.2
6690
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.178
0.2
1166
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
0.124
0.2
2
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.226
0.2
102
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.161
0.2
50
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.52
1.5
5974
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.289
2
9543
X-RAY DIFFRACTION
r_scbond_it
3.208
3
4128
X-RAY DIFFRACTION
r_scangle_it
4.393
4.5
3657
X-RAY DIFFRACTION
r_rigid_bond_restr
1.995
3
10102
X-RAY DIFFRACTION
r_sphericity_free
6.274
3
1179
X-RAY DIFFRACTION
r_sphericity_bonded
4.446
3
9300
LS refinement shell
Resolution: 1.53→1.57 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.258
396
-
Rwork
0.178
7702
-
obs
-
1198
68.98 %
+
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