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Structure of human hydroxyacid oxidase 1 bound with 6-amino-1-benzyl-5-(methylamino)pyrimidine-2,4(1H,3H)-dione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GMB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M MIB, pH 7, 30% PEG1000
Crystal Properties Matthews coefficient Solvent content 2.37 48.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.13 α = 90 b = 97.13 β = 90 c = 80.84 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2019-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.37 68.68 98.1 0.033 0.036 0.014 1 20.3 5.5 77168
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.37 1.41 82.3 0.819 0.994 0.547 0.523 2.8
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 6GMB 1.37 68.68 73234 3937 98.07 0.1808 0.1799 0.1792 0.196 0.1955 RANDOM 22.088
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] -0.41 -0.41 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.266 r_dihedral_angle_4_deg 16.814 r_dihedral_angle_3_deg 12.238 r_dihedral_angle_1_deg 7.231 r_angle_refined_deg 2.488 r_angle_other_deg 1.721 r_chiral_restr 0.183 r_bond_refined_d 0.023 r_gen_planes_refined 0.015 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.266 r_dihedral_angle_4_deg 16.814 r_dihedral_angle_3_deg 12.238 r_dihedral_angle_1_deg 7.231 r_angle_refined_deg 2.488 r_angle_other_deg 1.721 r_chiral_restr 0.183 r_bond_refined_d 0.023 r_gen_planes_refined 0.015 r_bond_other_d 0.005 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2538 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing