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Crystal structure of Pediococcus acidilactici lactate oxidase A94G mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J6X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 1.1M Sodium Malonate, 0.1M Hepes pH 7.0, 0.5% Jeffamine ED-2003.
Crystal Properties Matthews coefficient Solvent content 3.45 64.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.53 α = 90 b = 135.53 β = 90 c = 124.86 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 PILATUS 6M-F 2018-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2 50 100 11.98 13.2 39425
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05
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 2J6X 2 45.92 37453 1972 99.96 0.15306 0.15186 0.1649 0.17512 0.1878 RANDOM 24.29
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] -1.32 -1.32 2.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.611 r_dihedral_angle_4_deg 21.371 r_dihedral_angle_3_deg 12.988 r_dihedral_angle_1_deg 6.36 r_long_range_B_refined 5.849 r_long_range_B_other 5.848 r_scangle_other 4.82 r_scbond_it 3.131 r_scbond_other 3.13 r_mcangle_other 2.347
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.611 r_dihedral_angle_4_deg 21.371 r_dihedral_angle_3_deg 12.988 r_dihedral_angle_1_deg 6.36 r_long_range_B_refined 5.849 r_long_range_B_other 5.848 r_scangle_other 4.82 r_scbond_it 3.131 r_scbond_other 3.13 r_mcangle_other 2.347 r_mcangle_it 2.346 r_mcbond_it 1.626 r_mcbond_other 1.623 r_angle_refined_deg 1.544 r_angle_other_deg 1.403 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 2786 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing