☰ Navigation Tabs
Crystal structure of Pediococcus acidilactici (Putative)lactate oxidase Refolded WT protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6R9V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 1.1M Sodium Malonate, 0.1M Hepes pH 7.0, 0.5% jeffamine ED-2003.
Crystal Properties Matthews coefficient Solvent content 3.63 66.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.5 α = 90 b = 135.5 β = 90 c = 125.69 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 2018-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.96770 ESRF ID30B
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 2.6 50 100 11.7 13.3 18301
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 2.6 2.67
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 6R9V 2.6 47.95 17433 868 99.91 0.18728 0.18585 0.1961 0.21514 0.1993 RANDOM 36.766
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] -1.45 -1.45 2.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.234 r_dihedral_angle_4_deg 21.417 r_dihedral_angle_3_deg 15.131 r_dihedral_angle_1_deg 7.02 r_long_range_B_refined 6.845 r_long_range_B_other 6.845 r_scangle_other 5.583 r_mcangle_it 3.66 r_mcangle_other 3.659 r_scbond_other 3.642
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.234 r_dihedral_angle_4_deg 21.417 r_dihedral_angle_3_deg 15.131 r_dihedral_angle_1_deg 7.02 r_long_range_B_refined 6.845 r_long_range_B_other 6.845 r_scangle_other 5.583 r_mcangle_it 3.66 r_mcangle_other 3.659 r_scbond_other 3.642 r_scbond_it 3.641 r_mcbond_other 2.522 r_mcbond_it 2.521 r_angle_refined_deg 1.68 r_angle_other_deg 1.303 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 2707 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing