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urate oxidase azaxanthine complex under 600 bar (60 MPa) of argon
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R51 dimer reconstructed from pdbid 1R51
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8 298 20 microLiter (17 mg/mL protein, BUFFER Tris/Acetate pH 8) mixed with 20 microLiter PEG 4000 8% (same pH)
Crystal Properties Matthews coefficient Solvent content 2.91 57.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.225 α = 90 b = 95.268 β = 90 c = 104.5 γ = 90
Symmetry Space Group P 21 21 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 2018-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.7712 ESRF ID30B
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 1.86 47.7 81.5 0.063 0.067 0.026 0.999 21.4 11.3 53842 12.8
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 1.86 1.9 20.1 0.182 0.222 0.151 0.95 2.8 3.1
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 dimer reconstructed from pdbid 1R51 1.86 47.68 51064 2726 81.2 0.164 0.162 0.1743 0.228 0.219 RANDOM 17.38
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.183 r_dihedral_angle_4_deg 18.06 r_dihedral_angle_3_deg 15.125 r_dihedral_angle_1_deg 7.938 r_angle_other_deg 1.303 r_angle_refined_deg 1.297 r_chiral_restr 0.059 r_gen_planes_refined 0.009 r_bond_refined_d 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.183 r_dihedral_angle_4_deg 18.06 r_dihedral_angle_3_deg 15.125 r_dihedral_angle_1_deg 7.938 r_angle_other_deg 1.303 r_angle_refined_deg 1.297 r_chiral_restr 0.059 r_gen_planes_refined 0.009 r_bond_refined_d 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4724 Nucleic Acid Atoms Solvent Atoms 546 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing