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Crystal structure of D-amino acid oxidase from Rasamsonia emersonii strain YA
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, HANGING DROP 8.5 295 PEG3350, Tris-HCl, sodium formate
Crystal Properties Matthews coefficient Solvent content 1.95 36.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.13 α = 90 b = 79.13 β = 90 c = 366.673 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 95 PIXEL DECTRIS PILATUS3 S 6M 2019-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 68.529 100 0.094 0.105 0.033 13.6 10.1 87291 87291
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 100 1.056 1.056 1.175 0.37 0.7 10
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3WGT 2 41.62 82916 4229 99.98 0.2082 0.2063 0.2458 0.233 RANDOM 42.243
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.147 r_dihedral_angle_4_deg 16.566 r_dihedral_angle_3_deg 15.585 r_dihedral_angle_1_deg 5.893 r_angle_refined_deg 1.321 r_chiral_restr 0.089 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10382 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PDB_EXTRACT data extraction MOLREP phasing