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Substrate and inhibitor complexes of ribose 5-phosphate isomerase from Vibrio vulnificus YJ016
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ENQ PDB ENTRY 3ENQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 8% PEG4000, 0.05M succinate, pH4.0, 0.18M ammonium sulfate, 10mM ribose 5-phosphate, pH7.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.062 α = 90 b = 77.062 β = 90 c = 189.258 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A PAL/PLS 4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1 1.5 50 64147 64147
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3ENQ 2 25 25330 1321 94.13 0.19563 0.19164 0.2007 0.27181 0.2532 RANDOM 7.944
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 -0.67 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.003 r_dihedral_angle_3_deg 16.656 r_dihedral_angle_4_deg 14.203 r_dihedral_angle_1_deg 6.687 r_scangle_it 2.865 r_scbond_it 1.852 r_angle_refined_deg 1.739 r_mcangle_it 1.093 r_mcbond_it 0.651 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.003 r_dihedral_angle_3_deg 16.656 r_dihedral_angle_4_deg 14.203 r_dihedral_angle_1_deg 6.687 r_scangle_it 2.865 r_scbond_it 1.852 r_angle_refined_deg 1.739 r_mcangle_it 1.093 r_mcbond_it 0.651 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.255 r_xyhbond_nbd_refined 0.221 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.204 r_chiral_restr 0.111 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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 Atoms Number Protein Atoms 3204 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction