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Human milk xanthine oxidoreductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FO4 PDB ENTRY 1FO4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 26% (W/V) PEG 4K, 0.1M SODIUM ACETATE, PH 6, 0.25M AMMONIUM ACETATE, 10MM DTT, 10% (W/V) GLUCOSE
Crystal Properties Matthews coefficient Solvent content 2.7 53.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197.734 α = 90 b = 197.734 β = 90 c = 285.538 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.5 30 98.2 0.12 3.6 4.4 75088 1.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.62 95.3 0.47 1.5 3.5
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1FO4 3.59 30.76 70696 3745 98.2 0.182 0.178 0.258 RANDOM 22.75
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 40.738 r_dihedral_angle_3_deg 25.79 r_dihedral_angle_4_deg 22.106 r_dihedral_angle_1_deg 15.08 r_scangle_it 3.993 r_angle_refined_deg 3.461 r_scbond_it 2.564 r_mcangle_it 1.759 r_mcbond_it 1.193 r_symmetry_vdw_refined 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.738 r_dihedral_angle_3_deg 25.79 r_dihedral_angle_4_deg 22.106 r_dihedral_angle_1_deg 15.08 r_scangle_it 3.993 r_angle_refined_deg 3.461 r_scbond_it 2.564 r_mcangle_it 1.759 r_mcbond_it 1.193 r_symmetry_vdw_refined 0.36 r_nbtor_refined 0.354 r_nbd_refined 0.317 r_chiral_restr 0.221 r_xyhbond_nbd_refined 0.218 r_symmetry_hbond_refined 0.182 r_bond_refined_d 0.045 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 39530 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 277
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALA data scaling AMoRE phasing