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urate oxidase under 130 bar of krypton
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IC1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8 291 20 microliters of protein+azaxanthin, pH 8 TRIS 0.05M mixed with 20 microliters TRIS 0.05M + 10 % (v:v) PEG 8000.
Crystal Properties Matthews coefficient Solvent content 2.97 58.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.25 α = 90 b = 94.94 β = 90 c = 104.08 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 100 PIXEL DECTRIS PILATUS 6M 2018-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.861 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 70.14 99.5 0.055 0.017 1 21.5 13.3 62225 15.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 98.4 0.58 0.21 3.4 12.4
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 FOURIER SYNTHESIS THROUGHOUT 6IC1 1.5 70.14 59041 3146 99.89 0.14177 0.14031 0.1444 0.16949 0.1728 RANDOM 22.257
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.266 r_dihedral_angle_3_deg 14.341 r_dihedral_angle_4_deg 11.288 r_long_range_B_refined 7.47 r_dihedral_angle_1_deg 7.458 r_long_range_B_other 6.763 r_scangle_other 4.798 r_scbond_it 3.249 r_scbond_other 3.248 r_mcangle_it 2.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.266 r_dihedral_angle_3_deg 14.341 r_dihedral_angle_4_deg 11.288 r_long_range_B_refined 7.47 r_dihedral_angle_1_deg 7.458 r_long_range_B_other 6.763 r_scangle_other 4.798 r_scbond_it 3.249 r_scbond_other 3.248 r_mcangle_it 2.816 r_mcangle_other 2.815 r_mcbond_it 1.942 r_mcbond_other 1.902 r_angle_refined_deg 1.775 r_angle_other_deg 1.538 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 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 2368 Nucleic Acid Atoms Solvent Atoms 511 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement cctbx.xfel data reduction XSCALE data scaling FFT phasing