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Crystal structure of O-succinylbenzoic acid synthetase from Staphylococcus aureus, cubic crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WUE PDB entry 1WUE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 1.8M Sodium malonate, PH 7.0, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.16 61.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.773 α = 90 b = 144.773 β = 90 c = 144.773 γ = 90
Symmetry Space Group I 21 3
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 MAR CCD 165 mm MIRRORS 2006-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97940 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.45 50 100 0.068 0.055 7.1 22.6 18662 18662 76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.54 100 0.58 0.47 3 22.9 1841
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1WUE 2.45 20 18011 18011 590 99.88 0.21276 0.21276 0.21115 0.2068 0.26081 0.2523 RANDOM 69.584
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.844 r_dihedral_angle_4_deg 28.558 r_dihedral_angle_3_deg 21.306 r_scangle_it 13.769 r_scbond_it 10.568 r_dihedral_angle_1_deg 9.501 r_mcangle_it 8.916 r_mcbond_it 6.264 r_angle_refined_deg 1.271 r_chiral_restr 0.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.844 r_dihedral_angle_4_deg 28.558 r_dihedral_angle_3_deg 21.306 r_scangle_it 13.769 r_scbond_it 10.568 r_dihedral_angle_1_deg 9.501 r_mcangle_it 8.916 r_mcbond_it 6.264 r_angle_refined_deg 1.271 r_chiral_restr 0.385 r_nbtor_refined 0.296 r_symmetry_hbond_refined 0.215 r_xyhbond_nbd_refined 0.176 r_nbd_refined 0.153 r_symmetry_vdw_refined 0.115 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 2739 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling