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Lytic polysaccharide monooxygenase from Cellvibrio japonicus - CjAA10B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RW7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 0.1 M Tris pH 8.5, 1 M diammonium hydrogen phosphate
Crystal Properties Matthews coefficient Solvent content 2.02 39.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.824 α = 90 b = 74.922 β = 102.095 c = 137.455 γ = 90
Symmetry Space Group P 1 21 1
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 12M 2019-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.9 75.12 99.5 0.068 0.088 0.055 0.999 11 4.6 119664
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 1.9 1.93 0.819 1.067 0.678 0.95 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 75.12 118691 5863 98.575 0.233 0.2304 0.226 0.2761 0.2726 27.191
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] -1.764 0.516 1.495 0.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.386 r_dihedral_angle_3_deg 11.616 r_dihedral_angle_2_deg 7.692 r_dihedral_angle_1_deg 7.531 r_lrange_it 4.151 r_lrange_other 4.102 r_scangle_it 2.608 r_scangle_other 2.608 r_mcangle_it 2.417 r_mcangle_other 2.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.386 r_dihedral_angle_3_deg 11.616 r_dihedral_angle_2_deg 7.692 r_dihedral_angle_1_deg 7.531 r_lrange_it 4.151 r_lrange_other 4.102 r_scangle_it 2.608 r_scangle_other 2.608 r_mcangle_it 2.417 r_mcangle_other 2.417 r_scbond_it 1.675 r_scbond_other 1.675 r_mcbond_it 1.588 r_mcbond_other 1.588 r_angle_refined_deg 1.261 r_angle_other_deg 0.466 r_nbd_refined 0.2 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.186 r_nbd_other 0.186 r_symmetry_xyhbond_nbd_refined 0.186 r_symmetry_nbd_refined 0.172 r_xyhbond_nbd_refined 0.156 r_symmetry_nbtor_other 0.081 r_metal_ion_refined 0.079 r_chiral_restr 0.064 r_symmetry_xyhbond_nbd_other 0.054 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13042 Nucleic Acid Atoms Solvent Atoms 878 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data collection