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Crystal Structure of Helicobacter pylori gamma-Glutamyltranspeptidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DBU PDB entry 2DBU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 200 mM HEPES, 25% PEG MME2000, 5 mg/mL protein, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.13 42.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.354 α = 90 b = 105.206 β = 91.99 c = 91.06 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 315 2006-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.90000 APS 14-BM-C
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 1.9 100 91.5 0.046 32.3 4.8 72974 72974 16.2
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 1.9 2.02 77.6 0.466 4.8 7605
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-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 2DBU 1.9 28.19 72974 72974 7385 91.5 0.197 0.1969 0.239 0.2388 RANDOM 31.9
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] -1.41 1.81 0.44 0.97
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_scangle_it 2.67 c_mcangle_it 1.9 c_scbond_it 1.84 c_angle_deg 1.3 c_mcbond_it 1.25 c_improper_angle_d 0.85 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8089 Nucleic Acid Atoms Solvent Atoms 590 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement REFMAC refinement PDB_EXTRACT data extraction ADSC data collection CNS phasing