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Crystal structure of exopolyphosphatase (PPX) from E. coli O157:H7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Map obtained from peak wavelength used for orientation corresponding to the present dataset.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 5% PEG350, 0.1M Na Citrate (pH 4.6) and 5% MPD., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.73 54.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.547 α = 90 b = 132.139 β = 105.1 c = 107.85 γ = 90
Symmetry Space Group P 1 21 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 2005-09-05 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 4 2005-10-02 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 0.9801 NSLS X8C 2 SYNCHROTRON NSLS BEAMLINE X29A 1.1 NSLS X29A
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 2.04 104.257 87.5 0.073 9.2 3.6 128211 119378 31.1
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 2.04 2.11 33.8 0.405 1.9 5533
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 Map obtained from peak wavelength used for orientation corresponding to the present dataset. 2.2 50 128211 121721 6490 97.96 0.2047 0.20477 0.20248 0.1991 0.2471 0.2406 RANDOM 35.081
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] -0.83 -1.26 1.39 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.344 r_dihedral_angle_3_deg 17.159 r_dihedral_angle_4_deg 16.56 r_dihedral_angle_1_deg 5.562 r_scangle_it 3.493 r_scbond_it 2.185 r_mcangle_it 1.381 r_angle_refined_deg 1.278 r_mcbond_it 0.884 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.344 r_dihedral_angle_3_deg 17.159 r_dihedral_angle_4_deg 16.56 r_dihedral_angle_1_deg 5.562 r_scangle_it 3.493 r_scbond_it 2.185 r_mcangle_it 1.381 r_angle_refined_deg 1.278 r_mcbond_it 0.884 r_nbtor_refined 0.301 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.143 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.093 r_symmetry_hbond_refined 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15835 Nucleic Acid Atoms Solvent Atoms 630 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SnB phasing MOLREP phasing