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Structural and biochemical characterization of Yfce, a phosphoesterase from E. coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 drop: 50 mM sodium Cacodylate pH 6.5, 5 mM Hepes pH 7.5, 0.1 M Ammonium sulfate, 10% PEG 4000, 0.25 M NaCl, 1 mM BME, 5 mg/ml protein; well: 0.1 M sodium Cacodylate pH 6.5, 0.2 M Ammonium sulfate, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.76 55.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.02 α = 90 b = 71.02 β = 90 c = 173.68 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 170 CCD MARRESEARCH Si 111 2003-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 0.979438 APS 5ID-B
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 2.2 20 100 0.095 5.9 5.7 48352 6 6 28.7
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) 2.2 2.32 100 0.294 2.5 5.7 7059
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 SIRAS THROUGHOUT 2.25 20 46454 46449 2361 100 0.215 0.213 0.213 0.1939 0.252 0.227 RANDOM 37.1
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.1 c_angle_d 1.5 c_improper_angle_d 0.99 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5649 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 38
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling SOLVE phasing CNS refinement CCP4 data scaling