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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 arabinose 5-phosphate, pH7.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.022 α = 90 b = 77.022 β = 90 c = 190.294 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 2 50 28464 28464
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 25929 1389 95.99 0.242 0.238 0.2131 0.314 0.2186 RANDOM 7.302
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 -0.85 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.149 r_dihedral_angle_3_deg 19.524 r_dihedral_angle_4_deg 13.658 r_dihedral_angle_1_deg 8.019 r_scangle_it 2.841 r_angle_refined_deg 2.194 r_scbond_it 2.13 r_mcangle_it 1.304 r_mcbond_it 0.879 r_symmetry_hbond_refined 0.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.149 r_dihedral_angle_3_deg 19.524 r_dihedral_angle_4_deg 13.658 r_dihedral_angle_1_deg 8.019 r_scangle_it 2.841 r_angle_refined_deg 2.194 r_scbond_it 2.13 r_mcangle_it 1.304 r_mcbond_it 0.879 r_symmetry_hbond_refined 0.359 r_nbtor_refined 0.319 r_symmetry_vdw_refined 0.316 r_xyhbond_nbd_refined 0.262 r_nbd_refined 0.26 r_chiral_restr 0.135 r_bond_refined_d 0.024 r_gen_planes_refined 0.008 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 Atoms Number Protein Atoms 3204 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction