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Structure of CagD from H. pylori pathogenicity island crystallized in the presence of Cu(II) ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CWX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 298 0.2 M MgCl2, 0.1 M Hepes pH 7, 20% PEG 6000, CuCl2 0.02M , VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.29 46.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.03 α = 90 b = 65.03 β = 90 c = 156.16 γ = 120
Symmetry Space Group P 62 2 2
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 MAR CCD 165 mm 2007-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97621 ESRF BM14
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 2.75 78.09 99.9 0.079 7.5 10.3 5757 5757 21.5
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) 2.75 2.85 99 0.459 1.7 10.7 796
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3CWX 2.75 56.34 5322 252 100 0.262 0.262 0.261 0.2682 0.307 0.2809 RANDOM 56.67
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] 4.09 2.05 4.09 -6.14
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.8 c_mcangle_it 2.531 c_scangle_it 1.837 c_angle_deg 1.59 c_mcbond_it 1.478 c_scbond_it 1.255 c_improper_angle_d 0.75 c_bond_d 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1075 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 1
Software Software Software Name Purpose MAR345dtb data collection PHASES phasing CNS refinement MOSFLM data reduction SCALA data scaling