3ENW

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 ribose 5-phosphate, pH7.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1943.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.062α = 90
b = 77.062β = 90
c = 189.258γ = 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
11.5506414764147

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 3ENQ22525330132194.130.195630.191640.27181RANDOM7.944
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]
-0.67-0.33-0.671
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.003
r_dihedral_angle_3_deg16.656
r_dihedral_angle_4_deg14.203
r_dihedral_angle_1_deg6.687
r_scangle_it2.865
r_scbond_it1.852
r_angle_refined_deg1.739
r_mcangle_it1.093
r_mcbond_it0.651
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.003
r_dihedral_angle_3_deg16.656
r_dihedral_angle_4_deg14.203
r_dihedral_angle_1_deg6.687
r_scangle_it2.865
r_scbond_it1.852
r_angle_refined_deg1.739
r_mcangle_it1.093
r_mcbond_it0.651
r_nbtor_refined0.311
r_symmetry_hbond_refined0.255
r_xyhbond_nbd_refined0.221
r_nbd_refined0.217
r_symmetry_vdw_refined0.204
r_chiral_restr0.111
r_bond_refined_d0.018
r_gen_planes_refined0.007
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 Atoms449
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction