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Crystal structure of puromycin hydrolase S511A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AZO PDB ENTRY 3AZO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 1.7M ammonium sulfate, 0.1M Tris-HCl
, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.29 62.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.11 α = 90 b = 142.62 β = 90 c = 156.3 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 RIGAKU JUPITER 210 2007-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
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 2.15 100 93 0.092 12.2 4.3 95945 95945 20.2
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 2.15 2.23 83.2 0.416 2.1 3.6 8464
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 3AZO 2.15 29.74 95702 95702 4814 93.2 0.188 0.188 0.1879 0.219 0.2186 RANDOM 27.7
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] -2.31 8.74 -6.44
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.2 c_scangle_it 2.73 c_scbond_it 1.93 c_mcangle_it 1.77 c_angle_deg 1.3 c_mcbond_it 1.15 c_improper_angle_d 0.83 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.2 c_scangle_it 2.73 c_scbond_it 1.93 c_mcangle_it 1.77 c_angle_deg 1.3 c_mcbond_it 1.15 c_improper_angle_d 0.83 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10054 Nucleic Acid Atoms Solvent Atoms 1009 Heterogen Atoms 25
Software Software Software Name Purpose BSS data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing