3ENV

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ENQPDB ENTRY 3ENQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52938% PEG4000, 0.05M succinate, pH4.0, 0.18M ammonium sulfate, 10mM arabinose 5-phosphate, pH7.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.244.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.022α = 90
b = 77.022β = 90
c = 190.294γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 4APAL/PLS4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12502846428464

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 3ENQ22525929138995.990.2420.2380.314RANDOM7.302
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]
-0.85-0.43-0.851.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.149
r_dihedral_angle_3_deg19.524
r_dihedral_angle_4_deg13.658
r_dihedral_angle_1_deg8.019
r_scangle_it2.841
r_angle_refined_deg2.194
r_scbond_it2.13
r_mcangle_it1.304
r_mcbond_it0.879
r_symmetry_hbond_refined0.359
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.149
r_dihedral_angle_3_deg19.524
r_dihedral_angle_4_deg13.658
r_dihedral_angle_1_deg8.019
r_scangle_it2.841
r_angle_refined_deg2.194
r_scbond_it2.13
r_mcangle_it1.304
r_mcbond_it0.879
r_symmetry_hbond_refined0.359
r_nbtor_refined0.319
r_symmetry_vdw_refined0.316
r_xyhbond_nbd_refined0.262
r_nbd_refined0.26
r_chiral_restr0.135
r_bond_refined_d0.024
r_gen_planes_refined0.008
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 Atoms128
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction