☰ Navigation Tabs
Bilirubin oxidase from Myrothecium verrucaria with G395T 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 3.5 291.15 20% (w/v) PEG 3350, 0.1 M succinic acid pH 3.5, protein concentration 10 mg/ml
Crystal Properties Matthews coefficient Solvent content 3.1 60.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.215 α = 90 b = 200.681 β = 90 c = 216.615 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 2.1 47.66 95.6 0.191 0.222 0.11 0.985 6.5 3.7 81954 -3.7 17.4
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 2.1 2.14 97.7 0.857 0.996 0.496 0.586 1.6 3.7
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 2.1 47.66 81954 4026 95.333 0.154 0.154 0.153 0.1619 0.197 0.1721 RANDOM SELECTION 21.047
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] 0.112 -0.582 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.117 r_dihedral_angle_4_deg 19.093 r_dihedral_angle_3_deg 13.02 r_dihedral_angle_1_deg 7.802 r_lrange_it 4.973 r_lrange_other 4.724 r_scangle_it 3.465 r_scangle_other 3.464 r_scbond_it 2.205 r_scbond_other 2.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.117 r_dihedral_angle_4_deg 19.093 r_dihedral_angle_3_deg 13.02 r_dihedral_angle_1_deg 7.802 r_lrange_it 4.973 r_lrange_other 4.724 r_scangle_it 3.465 r_scangle_other 3.464 r_scbond_it 2.205 r_scbond_other 2.205 r_mcangle_it 2.159 r_mcangle_other 2.159 r_angle_refined_deg 1.633 r_mcbond_it 1.42 r_mcbond_other 1.417 r_angle_other_deg 1.316 r_symmetry_nbd_refined 0.246 r_nbd_refined 0.201 r_symmetry_nbd_other 0.187 r_nbd_other 0.181 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.168 r_xyhbond_nbd_refined 0.157 r_symmetry_xyhbond_nbd_other 0.13 r_symmetry_nbtor_other 0.081 r_metal_ion_refined 0.078 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8494 Nucleic Acid Atoms Solvent Atoms 1139 Heterogen Atoms 269
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing