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Bilirubin oxidase from Myrothecium verrucaria, mutant W396A in complex with ferricyanide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I3J D_1200011284
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.1 291.15 14% (w/v) PEG 3350, 0.1 M succinic acid, protein concentration 25 mg/ml
Crystal Properties Matthews coefficient Solvent content 3.2 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.906 α = 90 b = 201.803 β = 90 c = 217.869 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 PILATUS 6M 2018-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 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 1.6 47.93 99.6 0.074 0.086 0.044 0.998 9.2 3.8 195423 -3.7 10.9
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 1.6 1.63 99.8 0.635 0.738 0.373 0.7 1.5 3.9
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 D_1200011284 1.6 47.93 195423 9580 99.55 0.13189 0.13122 0.1314 0.15402 0.1434 Random selection 15.546
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] 0.15 -0.09 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.014 r_dihedral_angle_4_deg 19.615 r_dihedral_angle_3_deg 11.367 r_dihedral_angle_1_deg 7.254 r_long_range_B_refined 5.357 r_long_range_B_other 4.467 r_scangle_other 2.835 r_scbond_it 1.886 r_scbond_other 1.886 r_angle_refined_deg 1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.014 r_dihedral_angle_4_deg 19.615 r_dihedral_angle_3_deg 11.367 r_dihedral_angle_1_deg 7.254 r_long_range_B_refined 5.357 r_long_range_B_other 4.467 r_scangle_other 2.835 r_scbond_it 1.886 r_scbond_other 1.886 r_angle_refined_deg 1.67 r_mcangle_it 1.555 r_mcangle_other 1.555 r_angle_other_deg 1.456 r_mcbond_it 1.08 r_mcbond_other 1.079 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 8468 Nucleic Acid Atoms Solvent Atoms 1670 Heterogen Atoms 333
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing