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Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) in complex with holo-ACP from Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GLL 2GLL and 1L0I experimental model PDB 1L0I 2GLL and 1L0I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP PEG 3350, sodium citrate
Crystal Properties Matthews coefficient Solvent content 3.57 69.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.705 α = 90 b = 127.705 β = 90 c = 127.705 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 150 CCD AGILENT ATLAS CCD 2007-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 1 Photon Factory BL-18B
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 2.55 50 99.7 49.5 10 22941
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2GLL and 1L0I 2.55 31.926 1.35 22857 2019 99.72 0.1936 0.19 0.2313 0.2219
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.471 f_angle_d 1.309 f_chiral_restr 0.049 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3048 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement HKL-2000 data collection HKL-2000 data processing PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling CNS phasing