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Structure of beta-ketoacyl-ACP synthase I (FabB) from Vibrio Cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OYT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 1.6 M Ammonium citrate
Crystal Properties Matthews coefficient Solvent content 2.38 48.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.756 α = 90 b = 88.654 β = 90 c = 167.258 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 CCD ADSC QUANTUM 210r MIRRORS 2013-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97927 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 27 94.3 0.05 0.055 0.024 16.3 4.9 51875
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 79 0.134 0.155 0.077 0.97 3.1 2125
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 3OYT 2.01 27 49221 2492 93.67 0.1503 0.149 0.1579 0.1767 0.1824 RANDOM 26.701
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] -0.22 0.85 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.218 r_dihedral_angle_4_deg 16.525 r_dihedral_angle_3_deg 13.193 r_dihedral_angle_1_deg 6.14 r_angle_refined_deg 1.591 r_mcangle_it 1.416 r_angle_other_deg 1.308 r_mcbond_it 0.867 r_mcbond_other 0.867 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.218 r_dihedral_angle_4_deg 16.525 r_dihedral_angle_3_deg 13.193 r_dihedral_angle_1_deg 6.14 r_angle_refined_deg 1.591 r_mcangle_it 1.416 r_angle_other_deg 1.308 r_mcbond_it 0.867 r_mcbond_other 0.867 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5936 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms
Software Software Software Name Purpose HKL-3000 data reduction MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data scaling