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Crystal structure of urate oxidase at 140 MPa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R51 PDB ENTRY 1R51
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 281 PEG 3350(6-10%), 50-100mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.9 57.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.18 α = 90 b = 95.63 β = 90 c = 104.65 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 IMAGE PLATE MARRESEARCH UNFOCUSED BEAM 2004-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.331 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 22.9 97.8 0.068 0.068 9.2 4.2 17696 3 3 30.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.42 95 0.255 0.255 2.6 4.3 2476
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 RIGID BODY THROUGHOUT PDB ENTRY 1R51 2.3 22.36 2 17696 16712 894 97.85 0.16412 0.16136 0.1649 0.21342 0.1581 RANDOM 27.108
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 41.374 r_dihedral_angle_3_deg 18.055 r_dihedral_angle_4_deg 14.863 r_dihedral_angle_1_deg 6.834 r_scangle_it 5.513 r_scbond_it 3.543 r_mcangle_it 2.388 r_angle_refined_deg 2.071 r_mcbond_it 1.462 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.374 r_dihedral_angle_3_deg 18.055 r_dihedral_angle_4_deg 14.863 r_dihedral_angle_1_deg 6.834 r_scangle_it 5.513 r_scbond_it 3.543 r_mcangle_it 2.388 r_angle_refined_deg 2.071 r_mcbond_it 1.462 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.231 r_symmetry_hbond_refined 0.224 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.181 r_chiral_restr 0.133 r_bond_refined_d 0.024 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2359 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement DENZO data reduction CCP4 data scaling