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Structure of the N-acetyl-D-glucosamine oxidase from Ralstonia Solanacearum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 19% PEG33350
0.19 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 2 50.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.958 α = 90 b = 105.009 β = 90 c = 120.671 γ = 90
Symmetry Space Group P 21 21 21
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 2021-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.5 48.14 99.7 0.08 0.09 0.039 0.998 12 5 178041
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 100 0.67 0.744 0.319 0.732 5.2
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 2Y08 1.5 45 169012 8912 99.65 0.1526 0.1512 0.1512 0.1778 0.1776 RANDOM 15.799
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] 0.05 -0.28 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.003 r_dihedral_angle_4_deg 18.66 r_dihedral_angle_3_deg 12.274 r_dihedral_angle_1_deg 7.126 r_angle_refined_deg 1.867 r_angle_other_deg 1.605 r_chiral_restr 0.105 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.003 r_dihedral_angle_4_deg 18.66 r_dihedral_angle_3_deg 12.274 r_dihedral_angle_1_deg 7.126 r_angle_refined_deg 1.867 r_angle_other_deg 1.605 r_chiral_restr 0.105 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7604 Nucleic Acid Atoms Solvent Atoms 1193 Heterogen Atoms 181
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction