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L-lactate oxidase with D-lactate
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 1.29 4.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.781 α = 90 b = 132.781 β = 90 c = 92.07 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 1.38 46.99 99.37 0.96 11.65 16.6 155462
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 1.38 1.429 0.56
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 1.38 46.99 155462 8242 99.09 0.19718 0.19583 0.1956 0.22361 0.2237 RANDOM 23.001
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] -0.04 -0.04 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.369 r_dihedral_angle_3_deg 13.813 r_dihedral_angle_4_deg 11.492 r_long_range_B_refined 10.93 r_long_range_B_other 10.656 r_dihedral_angle_1_deg 8.031 r_scangle_other 4.608 r_mcangle_it 4.289 r_mcangle_other 4.288 r_scbond_it 3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.369 r_dihedral_angle_3_deg 13.813 r_dihedral_angle_4_deg 11.492 r_long_range_B_refined 10.93 r_long_range_B_other 10.656 r_dihedral_angle_1_deg 8.031 r_scangle_other 4.608 r_mcangle_it 4.289 r_mcangle_other 4.288 r_scbond_it 3 r_scbond_other 3 r_mcbond_it 2.783 r_mcbond_other 2.783 r_angle_refined_deg 1.848 r_angle_other_deg 1.538 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 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