2V1L

Structure of the conserved hypothetical protein VC1805 from pathogenicity island VPI-2 of Vibrio cholerae O1 biovar eltor str. N16961 shares structural homology with the human P32 protein


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details pH 7.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.31 α = 90
b = 78.31 β = 90
c = 42.29 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 -- ESRF ID14-1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.13 39.16 99.0 0.06 -- -- 8.8 -- 8131 -- 2.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.13 2.25 99.0 0.38 -- 6.4 9.0 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MIRAS 2.13 39.16 -- -- -- 8131 409 99.3 -- 0.239 0.235 0.316 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.13 2.19 -- 32 586 0.247 0.347 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.21
Anisotropic B[1][1] -0.25
Anisotropic B[1][2] -0.13
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.38
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 15.765
r_gen_planes_refined 0.006
r_scbond_it 1.998
r_chiral_restr 0.099
r_xyhbond_nbd_refined 0.178
r_scangle_it 2.924
r_dihedral_angle_4_deg 15.619
r_nbtor_refined 0.311
r_symmetry_vdw_refined 0.354
r_nbd_refined 0.229
r_dihedral_angle_1_deg 7.303
r_mcangle_it 1.987
r_angle_refined_deg 1.386
r_dihedral_angle_2_deg 38.612
r_symmetry_hbond_refined 0.214
r_bond_refined_d 0.013
r_mcbond_it 1.135
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1054
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 35

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
MOSFLM data reduction
SCALA data scaling
SOLVE/RESOLVE phasing