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Structural genomics, Crystal structure of Glycerophosphoryl diester phosphodiesterase from E. coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 16% PEG8000, 20% glycerol, 80 nM Na Cacodylate buffer, 0.16M Mg Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.958 56.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.759 α = 90 b = 118.386 β = 90 c = 242.048 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 SBC-2 mirrors 2003-11-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9795, 0.9798, 0.94656 APS 19-ID
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 50 94.8 0.086 18.83 5.2 239258 226817 2 4 15.4
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 2.07 63.5 0.524 1.68 4.1 23943
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2 43.56 122641 109764 10978 89.5 0.235 0.233 0.233 0.2331 0.265 0.2653 RANDOM 35.3
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] -2.4 11.33 -8.93
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.5 c_scangle_it 3.52 c_mcangle_it 2.53 c_scbond_it 2.5 c_mcbond_it 1.66 c_angle_deg 1.4 c_improper_angle_d 0.88 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10637 Nucleic Acid Atoms Solvent Atoms 1160 Heterogen Atoms 70
Software Software Software Name Purpose CNS refinement SBC-Collect data collection HKL-2000 data scaling CNS phasing