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Bilirubin oxidase from Myrothecium verrucaria, mutant W396F
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 3.1 60.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.25 α = 90 b = 200.663 β = 90 c = 217.121 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 Bruker PHOTON II HELIOS optics for MetalJet 2018-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE Excillum MetalJet D2 70 kV 1.3418
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 45.54 97.3 0.188 0.212 0.095 0.99 7.3 4.8 83782 -3.7 16.7
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 82.4 0.649 0.759 0.386 0.697 2.1 3.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT D_1200011284 2.1 45.54 83773 4179 97.22 0.16064 0.15945 0.19594 0.1459 Random selection 19.839
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] -0.01 -0.17 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.352 r_dihedral_angle_4_deg 20.17 r_dihedral_angle_3_deg 12.379 r_dihedral_angle_1_deg 7.635 r_long_range_B_refined 4.978 r_long_range_B_other 4.621 r_scangle_other 3.168 r_scbond_it 2.007 r_scbond_other 2.007 r_mcangle_it 1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.352 r_dihedral_angle_4_deg 20.17 r_dihedral_angle_3_deg 12.379 r_dihedral_angle_1_deg 7.635 r_long_range_B_refined 4.978 r_long_range_B_other 4.621 r_scangle_other 3.168 r_scbond_it 2.007 r_scbond_other 2.007 r_mcangle_it 1.97 r_mcangle_other 1.97 r_angle_refined_deg 1.539 r_angle_other_deg 1.299 r_mcbond_it 1.289 r_mcbond_other 1.283 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 8480 Nucleic Acid Atoms Solvent Atoms 1263 Heterogen Atoms 233
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing