☰ Navigation Tabs
L-lactate oxidase with pyruvate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DU2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 20 mg/ml in 50 mM sodium acetate (pH4.5) , 40% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 1.25 1.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.604 α = 90 b = 132.604 β = 90 c = 91.766 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 EIGER X 16M 2020-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.41 46.93 99.75 0.963 16.75 17.6 143078
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.41 1.464 0.591
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 2DU2 1.41 46.93 143078 7774 99.75 0.19455 0.19337 0.1934 0.21608 0.2162 RANDOM 25.871
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 32.751 r_dihedral_angle_3_deg 13.935 r_long_range_B_refined 11.077 r_long_range_B_other 10.841 r_dihedral_angle_4_deg 10.808 r_dihedral_angle_1_deg 7.689 r_mcangle_it 4.32 r_mcangle_other 4.319 r_scangle_other 4.312 r_scbond_it 2.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.751 r_dihedral_angle_3_deg 13.935 r_long_range_B_refined 11.077 r_long_range_B_other 10.841 r_dihedral_angle_4_deg 10.808 r_dihedral_angle_1_deg 7.689 r_mcangle_it 4.32 r_mcangle_other 4.319 r_scangle_other 4.312 r_scbond_it 2.842 r_scbond_other 2.842 r_mcbond_other 2.792 r_mcbond_it 2.791 r_angle_refined_deg 1.839 r_angle_other_deg 1.519 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5682 Nucleic Acid Atoms Solvent Atoms 740 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing