☰ Navigation Tabs
Bilirubin oxidase from Myrothecium verrucaria in complex with NAD+
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, HANGING DROP 3.1 291.15 14% (w/v) PEG 3350, 0.1 M succinic acid, pH 3.1, protein concentration 25 mg/ml.
Crystal Properties Matthews coefficient Solvent content 3.2 61.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.727 α = 90 b = 202.441 β = 90 c = 224.762 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 2013-05-30 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 46.992 98.9 0.115 0.128 0.055 0.993 10.2 5.4 87859 -3.7 26.5
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 90.9 0.692 0.782 0.354 0.723 2 4.5
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 46.992 87858 4435 98.749 0.169 0.1686 0.1692 0.176 0.2152 0.1878 RANDOM SELECTION 32.582
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] -1.683 0.052 1.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.266 r_dihedral_angle_4_deg 20.435 r_dihedral_angle_3_deg 13.513 r_dihedral_angle_1_deg 7.804 r_lrange_it 6.166 r_lrange_other 6.031 r_scangle_it 4.563 r_scangle_other 4.563 r_mcangle_it 3.53 r_mcangle_other 3.529
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.266 r_dihedral_angle_4_deg 20.435 r_dihedral_angle_3_deg 13.513 r_dihedral_angle_1_deg 7.804 r_lrange_it 6.166 r_lrange_other 6.031 r_scangle_it 4.563 r_scangle_other 4.563 r_mcangle_it 3.53 r_mcangle_other 3.529 r_scbond_it 3.134 r_scbond_other 3.128 r_mcbond_it 2.594 r_mcbond_other 2.589 r_angle_refined_deg 1.684 r_angle_other_deg 1.292 r_symmetry_nbd_refined 0.229 r_nbd_refined 0.201 r_nbd_other 0.198 r_symmetry_nbd_other 0.193 r_symmetry_xyhbond_nbd_refined 0.193 r_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.172 r_metal_ion_refined 0.171 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.079 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8476 Nucleic Acid Atoms Solvent Atoms 1013 Heterogen Atoms 295
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing