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Crystal structure of H.pylori ClpP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TYF PDB ENTRY 1TYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 287 32% PEG400, 0.1M HEPES, 0.35M magnesium chloride, pH 7.5, Microbatch, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.39 48.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.563 α = 90 b = 166.225 β = 90 c = 187.225 γ = 90
Symmetry Space Group P 21 21 21
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 BRUKER PROTEUM 300 2005-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6B 1.12714 PAL/PLS 6B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 20 82258 40.7
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 (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 1TYF 2.6 19.72 79160 7919 88.6 0.231 0.231 0.2324 0.299 0.3011 RANDOM 39.3
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] 7.4 -4.01 -3.4
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 c_scangle_it 2.82 c_mcangle_it 2.08 c_scbond_it 1.93 c_angle_deg 1.3 c_mcbond_it 1.26 c_improper_angle_d 0.83 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 c_scangle_it 2.82 c_mcangle_it 2.08 c_scbond_it 1.93 c_angle_deg 1.3 c_mcbond_it 1.26 c_improper_angle_d 0.83 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18410 Nucleic Acid Atoms Solvent Atoms 509 Heterogen Atoms
Software Software Software Name Purpose CNS refinement PROTEUM PLUS data collection HKL-2000 data reduction HKL-2000 data scaling EPMR phasing