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Serial crystallography structure of cofactor-free urate oxidase in complex with the 5-peroxo derivative of 9-methyl uric acid at room temperature
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CW2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.6 291 TRIS-ACETATE, PEG 8000, MUA,
Crystal Properties Matthews coefficient Solvent content 3.01 59.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.79 α = 90 b = 96.03 β = 90 c = 105.21 γ = 90
Symmetry Space Group I 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 293 PIXEL DECTRIS PILATUS3 6M 2019-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03 PETRA III, DESY P11
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (All) 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 2.3 17.07 99.98 0.849 0.3668 2.44 28.2 18280
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 100 0.225 1.9369 0.52 20.6
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 4CW2 2.3 17.07 18280 919 99.64 0.221 0.2182 0.222 0.2661 0.266 36.703
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] 1.332 -0.446 -0.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.473 r_dihedral_angle_3_deg 14.087 r_dihedral_angle_4_deg 13.027 r_dihedral_angle_1_deg 6.931 r_lrange_it 4.195 r_lrange_other 4.194 r_mcangle_other 2.81 r_mcangle_it 2.809 r_scangle_it 2.67 r_scangle_other 2.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.473 r_dihedral_angle_3_deg 14.087 r_dihedral_angle_4_deg 13.027 r_dihedral_angle_1_deg 6.931 r_lrange_it 4.195 r_lrange_other 4.194 r_mcangle_other 2.81 r_mcangle_it 2.809 r_scangle_it 2.67 r_scangle_other 2.67 r_mcbond_it 1.612 r_mcbond_other 1.611 r_scbond_it 1.522 r_scbond_other 1.522 r_angle_other_deg 1.438 r_angle_refined_deg 1.388 r_nbd_other 0.207 r_nbd_refined 0.203 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.125 r_symmetry_nbd_refined 0.123 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.071 r_ext_dist_refined_d 0.009 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2359 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing