☰ Navigation Tabs
Structure of human hydroxyacid oxidase 1 bound with 2-((4H-1,2,4-triazol-3-yl)thio)-1-(4-(3-chlorophenyl)piperazin-1-yl)ethan-1-one
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 2.35 47.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.06 α = 90 b = 97.06 β = 90 c = 80.22 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 1.29 61.91 95 0.047 0.051 0.02 0.999 15.6 5 88617
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 1.29 1.32 66.2 0.576 0.786 0.531 0.571 1.5
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 6GMB 1.5 61.91 56358 3040 99.89 0.1644 0.1632 0.1838 0.1984 RANDOM 16.839
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] -0.63 -0.63 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.031 r_dihedral_angle_4_deg 14.607 r_dihedral_angle_3_deg 12.266 r_dihedral_angle_1_deg 6.701 r_angle_refined_deg 1.954 r_angle_other_deg 1.555 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.031 r_dihedral_angle_4_deg 14.607 r_dihedral_angle_3_deg 12.266 r_dihedral_angle_1_deg 6.701 r_angle_refined_deg 1.954 r_angle_other_deg 1.555 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2578 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing