☰ Navigation Tabs
Crystal structure of Enterococcus hirae L-lactate oxidase M207L in complex with D-lactate form ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M73
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 Tris, PEG MME
Crystal Properties Matthews coefficient Solvent content 3.79 67.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.13 α = 90 b = 138.13 β = 90 c = 127.36 γ = 90
Symmetry Space Group I 4 2 2
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 2018-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.52 19.54 99.9 0.061 0.063 0.999 26.96 13.104 93906 23.83
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.56 99.9 0.703 0.731 0.942 4.36 13.078
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 6M73 1.52 19.54 89192 4714 99.91 0.1287 0.1279 0.1278 0.1444 0.1439 RANDOM 16.448
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] -0.54 -0.54 1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.809 r_dihedral_angle_4_deg 17.172 r_dihedral_angle_3_deg 11.775 r_dihedral_angle_1_deg 6.047 r_rigid_bond_restr 5.563 r_angle_other_deg 1.457 r_angle_refined_deg 1.387 r_chiral_restr 0.075 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.809 r_dihedral_angle_4_deg 17.172 r_dihedral_angle_3_deg 11.775 r_dihedral_angle_1_deg 6.047 r_rigid_bond_restr 5.563 r_angle_other_deg 1.457 r_angle_refined_deg 1.387 r_chiral_restr 0.075 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2783 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MOLREP phasing