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Bilirubin oxidase from Myrothecium verrucaria in complex with ATP
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 3.5 291.15 14% (w/v) PEG 3350, 0.1 M citric acid, pH 3.5; protein concentration 25 mg/ml
Crystal Properties Matthews coefficient Solvent content 3.2 61.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.468 α = 90 b = 204.726 β = 90 c = 221.388 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2012-05-29 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 2.4 46.95 90.4 0.122 0.139 0.065 0.992 10.5 4.2 106801 -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 2.4 2.44 93.6 0.636 0.73 0.346 0.689 2.2 4.1
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 2.4 46.499 106800 5384 89.841 0.17 0.16969 0.1701 0.1757 0.22425 0.1881 RANDOM SELECTION 28.048
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] 0.513 -0.883 0.369
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.107 r_dihedral_angle_4_deg 18.772 r_dihedral_angle_3_deg 13.903 r_dihedral_angle_1_deg 8.384 r_lrange_it 6.123 r_lrange_other 6.093 r_scangle_it 4.222 r_scangle_other 4.222 r_mcangle_it 3.591 r_mcangle_other 3.591
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.107 r_dihedral_angle_4_deg 18.772 r_dihedral_angle_3_deg 13.903 r_dihedral_angle_1_deg 8.384 r_lrange_it 6.123 r_lrange_other 6.093 r_scangle_it 4.222 r_scangle_other 4.222 r_mcangle_it 3.591 r_mcangle_other 3.591 r_scbond_it 2.678 r_scbond_other 2.678 r_mcbond_it 2.341 r_mcbond_other 2.34 r_angle_refined_deg 1.775 r_angle_other_deg 1.252 r_nbd_other 0.237 r_symmetry_nbd_refined 0.236 r_nbd_refined 0.197 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.169 r_metal_ion_refined 0.144 r_symmetry_xyhbond_nbd_refined 0.133 r_symmetry_xyhbond_nbd_other 0.092 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.072 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 16962 Nucleic Acid Atoms Solvent Atoms 1465 Heterogen Atoms 398
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing