☰ Navigation Tabs
Substrate and inhibitor complexes of ribose 5-phosphate isomerase A from Vibrio vulnificus YJ016
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O8B PDB ENTRY 1O8B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 8% PEG 4000, 0.05M succinate pH4.0, 0.18M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.094 α = 90 b = 77.094 β = 90 c = 189.995 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 CCD ADSC QUANTUM 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 1 PAL/PLS 4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.49 50 99.6 0.086 8.8 10.3 68818 68818
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.49 1.54 97.5 0.153
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 1O8B 2 25 26978 1480 99.98 0.22203 0.21924 0.2216 0.2728 0.2757 RANDOM 23.433
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 -1.28 1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.724 r_dihedral_angle_3_deg 16.982 r_dihedral_angle_4_deg 14.052 r_dihedral_angle_1_deg 7.218 r_scangle_it 4.333 r_scbond_it 2.949 r_angle_refined_deg 2.08 r_mcangle_it 1.931 r_mcbond_it 1.255 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.724 r_dihedral_angle_3_deg 16.982 r_dihedral_angle_4_deg 14.052 r_dihedral_angle_1_deg 7.218 r_scangle_it 4.333 r_scbond_it 2.949 r_angle_refined_deg 2.08 r_mcangle_it 1.931 r_mcbond_it 1.255 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.225 r_chiral_restr 0.161 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.155 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 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 Atoms Number Protein Atoms 3204 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction