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R92A mutant of Bacillus subtilis Oxalate Decarboxylase OxdC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UW8 PDB ENTRY 1UW8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 8-15% PEG 8000, 0.1 M TRIS PH8.5, 0-15% XYLITOL
Crystal Properties Matthews coefficient Solvent content 3.1 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.486 α = 90 b = 154.486 β = 90 c = 122.301 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 IMAGE PLATE MARRESEARCH OSMIC CONFOCAL MIRRORS 2004-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.8 28.04 99.9 0.16 13.41 7.75 13947 31.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.82 100 0.35 6.1 7.63
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 1UW8 2.8 28.12 13947 716 100 0.138 0.134 0.1332 0.211 0.208 RANDOM 14.06
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] -0.737 -0.369 -0.737 1.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.582 r_dihedral_angle_4_deg 20.228 r_dihedral_angle_3_deg 15.286 r_dihedral_angle_1_deg 6.719 r_scangle_it 3.234 r_scbond_it 1.961 r_angle_refined_deg 1.612 r_mcangle_it 1.178 r_mcbond_it 0.691 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.582 r_dihedral_angle_4_deg 20.228 r_dihedral_angle_3_deg 15.286 r_dihedral_angle_1_deg 6.719 r_scangle_it 3.234 r_scbond_it 1.961 r_angle_refined_deg 1.612 r_mcangle_it 1.178 r_mcbond_it 0.691 r_nbtor_refined 0.317 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.161 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2994 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing