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Structure of Pediococcus acidilactici putative lactate oxidase WT protein
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 293.15 1.1 M Sodium Malonate, 0.1 M Hepes pH 7.0, 0.5% Jeffamine ED-2003
Crystal Properties Matthews coefficient Solvent content 3.59 65.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.24 α = 90 b = 135.24 β = 90 c = 124.84 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 2M 2017-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.980 ESRF MASSIF-1
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 1.9 95.63 99.9 10.3 8.9 45969
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 1.928 1.895
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2J6X 1.9 91.9 43658 2311 99.9 0.19145 0.18993 0.22093 0.2049 RANDOM 28.168
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] -1.97 -1.97 3.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.935 r_dihedral_angle_4_deg 18.518 r_dihedral_angle_3_deg 14.828 r_dihedral_angle_1_deg 6.742 r_long_range_B_refined 6.686 r_long_range_B_other 6.653 r_scangle_other 5.245 r_scbond_it 3.435 r_scbond_other 3.434 r_mcangle_other 2.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.935 r_dihedral_angle_4_deg 18.518 r_dihedral_angle_3_deg 14.828 r_dihedral_angle_1_deg 6.742 r_long_range_B_refined 6.686 r_long_range_B_other 6.653 r_scangle_other 5.245 r_scbond_it 3.435 r_scbond_other 3.434 r_mcangle_other 2.827 r_mcangle_it 2.823 r_mcbond_it 1.959 r_mcbond_other 1.954 r_angle_refined_deg 1.628 r_angle_other_deg 1.37 r_chiral_restr 0.074 r_bond_refined_d 0.01 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 2787 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing