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Crystal structure of 5-hydroxyisourate hydrolase (formerly known as TRP, transthyretin related protein)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H1X pdb entry 2H1X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 20% (w/v) PEG 10000, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.4 48.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.324 α = 90 b = 66.737 β = 90 c = 237.393 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 2006-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.92 ESRF ID14-1
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 1.7 118 92.5 0.063 7.2 2.8 103601 103601
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 1.7 1.79 80.2 0.236 3 2.2 12933
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2H1X 1.7 64.2 103553 98390 5163 91.34 0.22537 0.22537 0.2238 0.2213 0.25493 0.2522 RANDOM 18.467
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] -0.27 0.19 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.397 r_dihedral_angle_4_deg 26.247 r_dihedral_angle_3_deg 12.327 r_dihedral_angle_1_deg 5.457 r_scangle_it 2.092 r_mcangle_it 1.998 r_scbond_it 1.449 r_mcbond_it 1.348 r_angle_refined_deg 1.206 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.397 r_dihedral_angle_4_deg 26.247 r_dihedral_angle_3_deg 12.327 r_dihedral_angle_1_deg 5.457 r_scangle_it 2.092 r_mcangle_it 1.998 r_scbond_it 1.449 r_mcbond_it 1.348 r_angle_refined_deg 1.206 r_nbtor_refined 0.323 r_symmetry_vdw_refined 0.276 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.189 r_symmetry_hbond_refined 0.145 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7208 Nucleic Acid Atoms Solvent Atoms 598 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection CCP4 data scaling MOLREP phasing