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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 1F41 PDB ENTRY 1F41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1 M HEPES, 20% PEG 10000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.06 40.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.078 α = 90 b = 64.135 β = 94 c = 58.937 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315 Toroidal mirror 2006-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.91 ESRF ID23-1
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 1.98 500 89.1 0.048 9.9 3.2 26947 26947
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) 1.98 2.09 89.1 0.19 3.5 2.9 3574
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1F41 1.98 58.82 0.19 26946 25579 1367 89.16 0.20809 0.20809 0.2057 0.2055 0.25168 0.2513 RANDOM 25.05
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] -0.45 0.61 0.23 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.694 r_dihedral_angle_4_deg 27.602 r_dihedral_angle_3_deg 14.15 r_dihedral_angle_1_deg 5.603 r_scangle_it 3.322 r_mcangle_it 3.126 r_scbond_it 2.349 r_mcbond_it 2.218 r_angle_refined_deg 1.159 r_nbtor_refined 0.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.694 r_dihedral_angle_4_deg 27.602 r_dihedral_angle_3_deg 14.15 r_dihedral_angle_1_deg 5.603 r_scangle_it 3.322 r_mcangle_it 3.126 r_scbond_it 2.349 r_mcbond_it 2.218 r_angle_refined_deg 1.159 r_nbtor_refined 0.327 r_symmetry_vdw_refined 0.301 r_symmetry_hbond_refined 0.26 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.218 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 3572 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction MOLREP phasing