3ENQ

Substrate and inhibitor complexes of ribose 5-phosphate isomerase A from Vibrio vulnificus YJ016


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O8BPDB ENTRY 1O8B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52938% PEG 4000, 0.05M succinate pH4.0, 0.18M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.244.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.094α = 90
b = 77.094β = 90
c = 189.995γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 4A1PAL/PLS4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.495099.60.0868.810.36881868818
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.491.5497.50.153

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1O8B22526978148099.980.222030.219240.2728RANDOM23.433
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]
-1.28-0.64-1.281.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.724
r_dihedral_angle_3_deg16.982
r_dihedral_angle_4_deg14.052
r_dihedral_angle_1_deg7.218
r_scangle_it4.333
r_scbond_it2.949
r_angle_refined_deg2.08
r_mcangle_it1.931
r_mcbond_it1.255
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.724
r_dihedral_angle_3_deg16.982
r_dihedral_angle_4_deg14.052
r_dihedral_angle_1_deg7.218
r_scangle_it4.333
r_scbond_it2.949
r_angle_refined_deg2.08
r_mcangle_it1.931
r_mcbond_it1.255
r_nbtor_refined0.303
r_symmetry_vdw_refined0.236
r_nbd_refined0.225
r_chiral_restr0.161
r_xyhbond_nbd_refined0.159
r_symmetry_hbond_refined0.155
r_bond_refined_d0.024
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3204
Nucleic Acid Atoms
Solvent Atoms65
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction