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Crystal structure of rat D428A mutant, urate bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AM9 PDB ENTRY 3AM9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 295 9-11% polyethylene glycol 8000, 0.6M Li2SO4, 5mM DTT, 1mM sodium salicylate, 0.4mM EDTA, 15% glycerol, 40mM HEPES (pH 6.20), VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.59 52.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.536 α = 90 b = 138.242 β = 90 c = 222.473 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 210 2008-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.73 42.4 300804 300756
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3AM9 1.73 42.35 294772 6032 95.48 0.16099 0.16024 0.1591 0.19754 0.1958 RANDOM 19.822
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] 0.06 0.04 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.899 r_dihedral_angle_4_deg 18.019 r_dihedral_angle_3_deg 13.435 r_dihedral_angle_1_deg 6.663 r_scangle_it 5.595 r_scbond_it 3.563 r_mcangle_it 2.257 r_angle_refined_deg 2.25 r_mcbond_it 1.38 r_chiral_restr 0.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.899 r_dihedral_angle_4_deg 18.019 r_dihedral_angle_3_deg 13.435 r_dihedral_angle_1_deg 6.663 r_scangle_it 5.595 r_scbond_it 3.563 r_mcangle_it 2.257 r_angle_refined_deg 2.25 r_mcbond_it 1.38 r_chiral_restr 0.182 r_bond_refined_d 0.028 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20012 Nucleic Acid Atoms Solvent Atoms 2570 Heterogen Atoms 170
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling