1R3D

Crystal structure of protein VC1974 from Vibrio cholerae, Pfam abhydrolase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829332% PEG 4000, .1M Tris pH 8.0, 10% Isopropanol, .24M Na Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2645.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.47α = 90
b = 99.47β = 90
c = 53.492γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152003-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 8-BM.978APS8-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9200.08918.32138121381-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.9799.50.416.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.9202135720222108998.250.181080.179320.21554RANDOM27.27
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.490.49-0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.752
r_dihedral_angle_4_deg20.881
r_dihedral_angle_3_deg14.429
r_dihedral_angle_1_deg5.82
r_scangle_it4.48
r_scbond_it3.061
r_mcangle_it1.74
r_angle_refined_deg1.439
r_mcbond_it1.385
r_angle_other_deg0.829
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.752
r_dihedral_angle_4_deg20.881
r_dihedral_angle_3_deg14.429
r_dihedral_angle_1_deg5.82
r_scangle_it4.48
r_scbond_it3.061
r_mcangle_it1.74
r_angle_refined_deg1.439
r_mcbond_it1.385
r_angle_other_deg0.829
r_mcbond_other0.276
r_symmetry_vdw_other0.249
r_nbd_refined0.234
r_nbd_other0.19
r_symmetry_vdw_refined0.186
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.141
r_symmetry_hbond_refined0.136
r_chiral_restr0.09
r_nbtor_other0.088
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1985
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing