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Bilirubin oxidase from Myrothecium verrucaria in complex with ferricyanide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XLL
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, protein concentration 25 mg/ml
Crystal Properties Matthews coefficient Solvent content 3.25 62.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.382 α = 90 b = 203.846 β = 90 c = 226.744 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 CCD MARMOSAIC 225 mm CCD 2011-11-25 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 2.59 47.3 100 0.144 0.157 0.061 0.994 13.5 6.5 48305 -3.7 30.7
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 2.59 2.67 99.9 0.858 0.963 0.428 0.608 2 4.9
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 2XLL 2.59 47.3 48305 2442 99.89 0.1618 0.1601 0.1678 0.2257 0.19 random selection 36.142
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] -0.47 -1.72 2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.954 r_dihedral_angle_4_deg 19.554 r_dihedral_angle_3_deg 14.747 r_dihedral_angle_1_deg 7.627 r_long_range_B_refined 6.017 r_long_range_B_other 6.004 r_scangle_other 4.194 r_mcangle_other 3.421 r_mcangle_it 3.42 r_scbond_it 2.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.954 r_dihedral_angle_4_deg 19.554 r_dihedral_angle_3_deg 14.747 r_dihedral_angle_1_deg 7.627 r_long_range_B_refined 6.017 r_long_range_B_other 6.004 r_scangle_other 4.194 r_mcangle_other 3.421 r_mcangle_it 3.42 r_scbond_it 2.808 r_scbond_other 2.808 r_mcbond_it 2.162 r_mcbond_other 2.159 r_angle_refined_deg 1.35 r_angle_other_deg 0.819 r_chiral_restr 0.059 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 8476 Nucleic Acid Atoms Solvent Atoms 547 Heterogen Atoms 357
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing