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The Crystal Structure of the Inactive Peptidase Domain of a Putative Zinc Protease from Bordetella parapertussis to 2.2A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 297 40% PEG 300, 0.1M Sodium cacodylate pH 6.5, 0.2M Calcium acetate, vapor diffusion, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.82 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.173 α = 90 b = 108.173 β = 90 c = 113.995 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 100 CCD ADSC QUANTUM 315 2009-07-14 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 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 2.1 50 99.6 0.099 10.3 4.4 28929
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 2.1 2.18 100 0.72 4.4 2896
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 THROUGHOUT 2.2 43.33 25100 1273 99.53 0.219 0.216 0.2307 0.258 0.2658 RANDOM 16.65
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] -0.07 -0.03 -0.07 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.865 r_dihedral_angle_4_deg 20.679 r_dihedral_angle_3_deg 18.877 r_dihedral_angle_1_deg 5.628 r_scangle_it 2.712 r_scbond_it 1.84 r_angle_refined_deg 1.442 r_mcangle_it 0.936 r_mcbond_it 0.518 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.865 r_dihedral_angle_4_deg 20.679 r_dihedral_angle_3_deg 18.877 r_dihedral_angle_1_deg 5.628 r_scangle_it 2.712 r_scbond_it 1.84 r_angle_refined_deg 1.442 r_mcangle_it 0.936 r_mcbond_it 0.518 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2752 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 14
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELX phasing MLPHARE phasing DM phasing ARP/wARP model building Coot model building