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E162A 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 3.2 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.749 α = 90 b = 154.749 β = 90 c = 122.124 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 2004-10-29 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 3.1 28.08 99.5 0.15 9.83 5.91 10285 33.28
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 3.1 3.13 99.9 0.28 6.2 5.91
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 3.1 27.91 10284 523 99.5 0.166 0.163 0.1579 0.219 0.2043 RANDOM 9.91
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] -1.33 -0.665 -1.33 1.995
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.174 r_dihedral_angle_4_deg 19.443 r_dihedral_angle_3_deg 14.579 r_dihedral_angle_1_deg 6.547 r_scangle_it 2.656 r_scbond_it 1.604 r_angle_refined_deg 1.504 r_mcangle_it 1.097 r_mcbond_it 0.64 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.174 r_dihedral_angle_4_deg 19.443 r_dihedral_angle_3_deg 14.579 r_dihedral_angle_1_deg 6.547 r_scangle_it 2.656 r_scbond_it 1.604 r_angle_refined_deg 1.504 r_mcangle_it 1.097 r_mcbond_it 0.64 r_nbtor_refined 0.316 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.168 r_symmetry_hbond_refined 0.124 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 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 2996 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing