☰ Navigation Tabs
1.2 A resolution structure of human hydroxyacid oxidase 1 bound with FMN and 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole
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 298 20% PEG3350 -- 10% ethylene glycol -- 0.1M bis-tris-propane pH 7.5 -- 0.2M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.38 48.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.348 α = 90 b = 97.348 β = 90 c = 80.363 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 1.2 68.835 99.5 0.076 0.088 0.042 8.9 4.2 115996 115996
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 1.2 1.26 99.5 0.688 0.688 0.793 0.386 1.1 4.1
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 2NZL 1.2 38.31 110271 5723 99.39 0.1352 0.1342 0.143 0.1548 0.1615 RANDOM 16.823
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] -0.22 -0.22 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.866 r_sphericity_free 21.469 r_dihedral_angle_4_deg 13.736 r_dihedral_angle_3_deg 11.812 r_sphericity_bonded 11.217 r_dihedral_angle_1_deg 6.665 r_angle_refined_deg 1.376 r_angle_other_deg 1.015 r_rigid_bond_restr 0.975 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.866 r_sphericity_free 21.469 r_dihedral_angle_4_deg 13.736 r_dihedral_angle_3_deg 11.812 r_sphericity_bonded 11.217 r_dihedral_angle_1_deg 6.665 r_angle_refined_deg 1.376 r_angle_other_deg 1.015 r_rigid_bond_restr 0.975 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2764 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction SCALA data scaling PHASER phasing XDS data reduction