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Crystal structure of a Glycerophosphodiester Phosphodiesterase from Staphylococcus aureus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.3 M Sodium citrate, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 3.24 62.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.164 α = 90 b = 115.164 β = 90 c = 451.335 γ = 120
Symmetry Space Group P 31 2 1
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 mirrors 2006-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97915 NSLS X4A
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 2.6 25 91 0.053 26.4 6.5 98343 98343 45.7
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 SAD THROUGHOUT 2.6 24.97 98343 98343 4954 91 0.249 0.249 0.249 0.2438 0.265 0.2604 RANDOM 60
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] 4.04 10.04 4.04 -8.08
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.5 c_scangle_it 2.95 c_mcangle_it 2.28 c_scbond_it 1.82 c_angle_deg 1.4 c_mcbond_it 1.3 c_improper_angle_d 0.83 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17488 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 56
Software Software Software Name Purpose CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling SHELXS phasing