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Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK (Apo-form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q8F YEIK PDB CODE 1Q8F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 25% PEG 3350, 0.1M TRIS PH 8.5, 0.2M SODIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.32 46.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.601 α = 66.65 b = 85.231 β = 79.39 c = 90.06 γ = 85.3
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 4 2005-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 2.2 81.65 94.8 0.112 0.112 10.8 3.3 58257
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) 2.2 2.32 94.5 0.363 0.363 3.2 3.2
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT YEIK PDB CODE 1Q8F 2.2 47.91 55302 2954 94.43 0.18687 0.18494 0.22284 0.202 RANDOM 24.962
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] 1.11 0.59 1.31 -1.2 0.04 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.862 r_dihedral_angle_3_deg 13.953 r_dihedral_angle_4_deg 10.723 r_dihedral_angle_1_deg 6.11 r_scangle_it 1.816 r_angle_refined_deg 1.321 r_scbond_it 1.267 r_angle_other_deg 1.101 r_mcangle_it 0.696 r_mcbond_it 0.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.862 r_dihedral_angle_3_deg 13.953 r_dihedral_angle_4_deg 10.723 r_dihedral_angle_1_deg 6.11 r_scangle_it 1.816 r_angle_refined_deg 1.321 r_scbond_it 1.267 r_angle_other_deg 1.101 r_mcangle_it 0.696 r_mcbond_it 0.457 r_symmetry_vdw_other 0.281 r_symmetry_vdw_refined 0.218 r_symmetry_hbond_refined 0.212 r_nbd_refined 0.204 r_nbd_other 0.187 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.167 r_mcbond_other 0.129 r_nbtor_other 0.086 r_chiral_restr 0.081 r_metal_ion_refined 0.07 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9129 Nucleic Acid Atoms Solvent Atoms 527 Heterogen Atoms 4
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling