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Crystal structure of beta-ketoacyl-ACP synthase III (FabH) from Vibrio Cholerae in complex with Coenzyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GYO PDB ENTRY 2GYO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289 0.2M calcium chloride, 20%PEG3350, VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.43 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.449 α = 90 b = 100.248 β = 90 c = 132.763 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 MAR scanner 300 mm plate MIRRORS 2013-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9792 APS 21-ID-G
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 1.78 50 97.6 0.091 25.2 6.8 125028 -3 19.6
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 1.78 1.81 87.8 0.817 2 5.4 5576
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2GYO 1.78 50 124893 6293 98 0.1715 0.1702 0.1957 0.1979 RANDOM 26.2697
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] -0.67 -1.44 2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.561 r_dihedral_angle_4_deg 16.302 r_dihedral_angle_3_deg 11.484 r_dihedral_angle_1_deg 5.751 r_angle_refined_deg 1.671 r_mcangle_it 1.66 r_angle_other_deg 1.067 r_mcbond_it 1.026 r_mcbond_other 1.026 r_chiral_restr 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.561 r_dihedral_angle_4_deg 16.302 r_dihedral_angle_3_deg 11.484 r_dihedral_angle_1_deg 5.751 r_angle_refined_deg 1.671 r_mcangle_it 1.66 r_angle_other_deg 1.067 r_mcbond_it 1.026 r_mcbond_other 1.026 r_chiral_restr 0.18 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9458 Nucleic Acid Atoms Solvent Atoms 1262 Heterogen Atoms 201
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling