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Bilirubin oxidase from Myrothecium verrucaria with R356S mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I3J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 2.5 291.15 20% (w/v) PEG 3350, 0.1 M malonic acid pH 2.5, protein concentration 10 mg/ml
Crystal Properties Matthews coefficient Solvent content 3.1 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.072 α = 90 b = 200.888 β = 90 c = 217.306 γ = 90
Symmetry Space Group F 2 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 PILATUS3 S 6M 2022-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 2.05 47.785 99 0.224 0.249 0.106 0.989 7 5.3 91634 -3.7 23.6
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 2.05 2.09 99.9 1.715 1.899 0.802 0.387 1 5.4
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-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 2.05 47.785 91631 4479 98.923 0.16 0.1598 0.1581 0.1686 0.2029 0.1803 RANDOM SELECTION 26.86
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] 0.477 -0.203 -0.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.822 r_dihedral_angle_4_deg 17.948 r_dihedral_angle_3_deg 12.492 r_dihedral_angle_1_deg 7.811 r_lrange_it 5.333 r_lrange_other 5.142 r_scangle_it 3.958 r_scangle_other 3.958 r_scbond_it 2.622 r_scbond_other 2.608
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.822 r_dihedral_angle_4_deg 17.948 r_dihedral_angle_3_deg 12.492 r_dihedral_angle_1_deg 7.811 r_lrange_it 5.333 r_lrange_other 5.142 r_scangle_it 3.958 r_scangle_other 3.958 r_scbond_it 2.622 r_scbond_other 2.608 r_mcangle_it 2.553 r_mcangle_other 2.552 r_mcbond_it 1.774 r_mcbond_other 1.774 r_angle_refined_deg 1.651 r_angle_other_deg 1.325 r_symmetry_nbd_refined 0.234 r_nbd_other 0.205 r_nbd_refined 0.203 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_other 0.117 r_metal_ion_refined 0.094 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8466 Nucleic Acid Atoms Solvent Atoms 1160 Heterogen Atoms 255
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing