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Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with sakuranetin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GLL PDB entry 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 Additive, 20%(w/v) Benzamidine HCl, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.17 61.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.967 α = 90 b = 100.312 β = 90 c = 186.57 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 2008-03-15 M 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 50 99.8 0.112 0.112 12.8 5.8 55059
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 0.409 0.409 3.3 5.5 43850
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 2GLL 2.4 19.99 54994 2793 99.78 0.191 0.19 0.193 0.212 0.2172 RANDOM 20.555
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] 0.49 -1.22 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.853 r_dihedral_angle_3_deg 14.839 r_dihedral_angle_4_deg 9.305 r_dihedral_angle_1_deg 5.487 r_scangle_it 1.886 r_angle_refined_deg 1.145 r_scbond_it 1.129 r_mcangle_it 0.815 r_mcbond_it 0.483 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.853 r_dihedral_angle_3_deg 14.839 r_dihedral_angle_4_deg 9.305 r_dihedral_angle_1_deg 5.487 r_scangle_it 1.886 r_angle_refined_deg 1.145 r_scbond_it 1.129 r_mcangle_it 0.815 r_mcbond_it 0.483 r_nbtor_refined 0.308 r_nbd_refined 0.187 r_symmetry_vdw_refined 0.158 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7272 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms 102
Software Software Software Name Purpose MOSFLM data reduction d*TREK data scaling MOLREP phasing CNS refinement REFMAC refinement PDB_EXTRACT data extraction