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Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK in complex with inosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q8F PDB ENTRY 1Q8F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1M Tris-HCl, 0.2M NaCl, 24% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.12 41.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.112 α = 67.9 b = 82.406 β = 79.59 c = 90.163 γ = 89.65
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ Osmic 2007-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.3 100 95.4 0.102 0.095 18.7 7.3 50148 50148 -3 28.3
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 2.3 2.45 92.6 0.255 0.235 8.9 6.7 5843
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 (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 1Q8F 2.3 81.92 48587 48587 1560 95.58 0.203 0.201 0.2022 0.255 0.2573 RANDOM 22.98
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] 1.19 0.54 0.51 -0.23 0.02 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.082 r_dihedral_angle_4_deg 17.026 r_dihedral_angle_3_deg 15.107 r_dihedral_angle_1_deg 6.368 r_scangle_it 4.728 r_scbond_it 3.759 r_mcangle_it 3.389 r_mcbond_it 2.516 r_angle_refined_deg 1.473 r_symmetry_vdw_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.082 r_dihedral_angle_4_deg 17.026 r_dihedral_angle_3_deg 15.107 r_dihedral_angle_1_deg 6.368 r_scangle_it 4.728 r_scbond_it 3.759 r_mcangle_it 3.389 r_mcbond_it 2.516 r_angle_refined_deg 1.473 r_symmetry_vdw_refined 0.303 r_nbtor_refined 0.301 r_symmetry_hbond_refined 0.259 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.163 r_metal_ion_refined 0.13 r_chiral_restr 0.092 r_bond_refined_d 0.016 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_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 9030 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection XDS data reduction XSCALE data scaling MOLREP phasing