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Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WGT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 10% PEG 3350, 15% MPD, 200 mM Lithium sulfate, 100 mM Bis-Tris-HCl pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.54 51.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.064 α = 90 b = 273.95 β = 90 c = 136.8 γ = 90
Symmetry Space Group C 2 2 21
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 DECTRIS EIGER X 4M 2015-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.10 Photon Factory BL-1A
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 3.2 144.49 100 0.111 0.121 13.3 6.9 52954
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 3.2 3.37 100 0.603 3.7 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3WGT 3.2 48.73 3 50291 2657 99.93 0.14979 0.14494 0.1523 0.24212 0.2411 RANDOM 77.419
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] 3.38 1.14 -4.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.725 r_dihedral_angle_3_deg 19.059 r_dihedral_angle_4_deg 16.577 r_long_range_B_refined 11.684 r_long_range_B_other 11.684 r_mcangle_it 8.324 r_mcangle_other 8.324 r_scangle_other 8.229 r_dihedral_angle_1_deg 7.523 r_mcbond_it 5.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.725 r_dihedral_angle_3_deg 19.059 r_dihedral_angle_4_deg 16.577 r_long_range_B_refined 11.684 r_long_range_B_other 11.684 r_mcangle_it 8.324 r_mcangle_other 8.324 r_scangle_other 8.229 r_dihedral_angle_1_deg 7.523 r_mcbond_it 5.279 r_mcbond_other 5.276 r_scbond_it 5.15 r_scbond_other 5.148 r_angle_refined_deg 1.687 r_angle_other_deg 1.022 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21640 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 697
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing