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Structure of human hydroxyacid oxidase 1 bound with FMN and glycolate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NZL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 30% PEG1000 -- 0.1M MIB pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.37 48.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.431 α = 90 b = 97.431 β = 90 c = 80.364 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 PILATUS3 S 6M 2018-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 1.35 68.894 99.2 0.04 0.043 0.017 29.2 6.2 81521 81521
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 1.35 1.42 94.9 0.093 0.093 0.107 0.052 7.2 3.9
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 2NZL 1.35 40.21 77545 3976 99.16 0.111 0.11 0.1302 0.156 RANDOM 14.354
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] -0.32 -0.32 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.515 r_sphericity_free 22.899 r_dihedral_angle_4_deg 13.054 r_dihedral_angle_3_deg 11.103 r_sphericity_bonded 8.307 r_dihedral_angle_1_deg 6.228 r_angle_refined_deg 1.258 r_angle_other_deg 0.987 r_rigid_bond_restr 0.743 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.515 r_sphericity_free 22.899 r_dihedral_angle_4_deg 13.054 r_dihedral_angle_3_deg 11.103 r_sphericity_bonded 8.307 r_dihedral_angle_1_deg 6.228 r_angle_refined_deg 1.258 r_angle_other_deg 0.987 r_rigid_bond_restr 0.743 r_chiral_restr 0.063 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2791 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction SCALA data scaling PHASER phasing XDS data reduction