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Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with compound 3m
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GLL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.8 277 0.1M Sodium Acetate trihydrate, 2.0 M Sodium Formate, 20% w/v Benzamidine HCl, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.18 61.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.07 α = 90 b = 100.55 β = 90 c = 186.487 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 IMAGE PLATE RIGAKU RAXIS IV++ 2007-06-11 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 93.25 98 0.149 0.149 4.7 5.1 47877
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.64 95.6 0.613 0.613 1.2 5.1 6740
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2GLL 2.5 15 47677 2379 97.8 0.201 0.237 0.1629 25.385
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] -1.09 5.99 -4.9
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.939 c_mcangle_it 1.956 c_scbond_it 1.948 c_mcbond_it 1.191
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7287 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 94
Software Software Software Name Purpose d*TREK data scaling SCALA data scaling MOLREP phasing CNS refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction CNS phasing