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Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with compound 3j
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, 2.0M Sodium Formate, 20% w/v Benzamidine HCl, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.17 61.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.97 α = 90 b = 100.323 β = 90 c = 186.417 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 2.4 93.25 99.8 0.074 0.074 8.3 6.3 55022
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) 2.4 2.53 100 0.193 0.193 3.8 6 7913
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2GLL 2.4 15 54802 2738 100 0.197 0.1932 0.23 0.1909 18.093
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] -1.516 4.429 -2.913
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.857 c_scbond_it 1.939 c_mcangle_it 1.625 c_mcbond_it 1.093
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7287 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 104
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