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E. coli beta-ketoacyl-[acyl carrier protein] synthase III (FabH) with an acetylated cysteine and in complex with oxa(dethia)-Coenzyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HNJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 75 mM Magnesium Chloride, 20% PEG 6000, 3% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.02 39.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.662 α = 90 b = 72.662 β = 90 c = 102.852 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD MARMOSAIC 300 mm CCD 2019-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) CC (Half) 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 1.302 22.992 99.6 0.068 0.05 0.019 0.998 113.7 14.2 68034 14.742
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.302 1.35 99.6 0.544 0.454 0.162 0.948 6.2 12
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 (All) 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 1HNJ 1.302 22.992 67957 3446 99.937 0.144 0.1427 0.1436 0.1668 0.1679 Random 14.742
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] -0.619 -0.619 1.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.389 r_dihedral_angle_4_deg 19.449 r_dihedral_angle_3_deg 11.639 r_dihedral_angle_1_deg 6.456 r_lrange_it 6.033 r_lrange_other 5.707 r_scangle_it 3.311 r_scangle_other 3.31 r_scbond_it 2.275 r_scbond_other 2.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.389 r_dihedral_angle_4_deg 19.449 r_dihedral_angle_3_deg 11.639 r_dihedral_angle_1_deg 6.456 r_lrange_it 6.033 r_lrange_other 5.707 r_scangle_it 3.311 r_scangle_other 3.31 r_scbond_it 2.275 r_scbond_other 2.274 r_angle_refined_deg 2.088 r_mcangle_other 1.79 r_mcangle_it 1.787 r_angle_other_deg 1.55 r_mcbond_it 1.248 r_mcbond_other 1.239 r_symmetry_xyhbond_nbd_refined 0.391 r_xyhbond_nbd_refined 0.295 r_symmetry_nbd_refined 0.256 r_nbd_other 0.222 r_nbd_refined 0.221 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.17 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.089 r_symmetry_xyhbond_nbd_other 0.06 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2358 Nucleic Acid Atoms Solvent Atoms 506 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction PHASER phasing ARP/wARP model building Coot model building HKL-2000 data reduction