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Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus anthraci
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P76 PDB entry 2p76
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 0.2 M litium sulfate, 0.1 M Tris pH 8.5, 30 %(w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.13 60.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.644 α = 90 b = 85.891 β = 121.33 c = 191.539 γ = 90
Symmetry Space Group C 1 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 315r mirrors 2012-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97937 APS 19-ID
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 2.5 50 99.1 0.137 22.4 3.6 95660 95660 33.28
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 2.5 2.55 97.4 0.678 2.8 3.1 4633
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 2p76 2.534 37.696 93834 93834 1965 96.92 0.155 0.155 0.154 0.1557 0.204 0.2037 random 41.2
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 f_dihedral_angle_d 14.546 f_angle_d 1.077 f_chiral_restr 0.043 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15688 Nucleic Acid Atoms Solvent Atoms 650 Heterogen Atoms 110
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 data collection HKL-3000 phasing MOLREP phasing PHENIX model building PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing