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urate oxidase under 2000 bar (220 MPa) of argon
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R56 1r56 reconstructed dimer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8 291 20 microliter of protein (15 mg/ml) mixed with 20 microliter of solution: Buffer Tris 0.05M (chloride free) + 4% PEG 4000.
Crystal Properties Matthews coefficient Solvent content 2.9 57.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.552 α = 90 b = 96.682 β = 90 c = 105.579 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 PILATUS3 S 6M 2016-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.77 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 1.723 71.322 93.8 0.057 0.062 0.017 0.999 22.8 11.4 72278
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 1.723 1.826 56.5 0.542 0.63 0.26 0.802 2 5.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1r56 reconstructed dimer 1.8 46.333 72278 3583 96.208 0.211 0.209 0.2091 0.2432 0.2433 34.255
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] -0.004 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.701 r_dihedral_angle_4_deg 18.603 r_dihedral_angle_3_deg 17.12 r_dihedral_angle_1_deg 8.192 r_lrange_it 6.921 r_scangle_it 5.941 r_scbond_it 4.836 r_mcangle_it 4.755 r_mcbond_it 4.021 r_angle_refined_deg 1.451
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.701 r_dihedral_angle_4_deg 18.603 r_dihedral_angle_3_deg 17.12 r_dihedral_angle_1_deg 8.192 r_lrange_it 6.921 r_scangle_it 5.941 r_scbond_it 4.836 r_mcangle_it 4.755 r_mcbond_it 4.021 r_angle_refined_deg 1.451 r_metal_ion_refined 0.34 r_nbtor_refined 0.317 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.193 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.116 r_symmetry_xyhbond_nbd_refined 0.106 r_gen_planes_refined 0.012 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4718 Nucleic Acid Atoms Solvent Atoms 491 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing