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Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MAS PDB entry 1MAS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 PEGMME 3350, methanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.32 47.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.808 α = 112.95 b = 85.707 β = 101.95 c = 90.678 γ = 85.92
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 Mirror 2003-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 81.6 91.5 0.046 9.5 2 122468 -3 -3 16.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 63.8 0.221 3 1.9 12529
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 1MAS 1.7 43.83 121220 121220 1247 91.53 0.1534 0.15348 0.15331 0.1532 0.16989 0.1682 RANDOM 15.208
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] 0.15 0.51 -0.28 -0.32 0.18 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.855 r_scangle_it 3.336 r_scbond_it 2.003 r_angle_refined_deg 1.307 r_mcangle_it 1.011 r_mcbond_it 0.566 r_symmetry_hbond_refined 0.201 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.14 r_symmetry_vdw_refined 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.855 r_scangle_it 3.336 r_scbond_it 2.003 r_angle_refined_deg 1.307 r_mcangle_it 1.011 r_mcbond_it 0.566 r_symmetry_hbond_refined 0.201 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.14 r_symmetry_vdw_refined 0.132 r_chiral_restr 0.093 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9260 Nucleic Acid Atoms Solvent Atoms 1055 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing