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Crystal structure of beta-ketoacyl synthase from Brucella melitensis in complex with platencin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LRF pdb entry 3LRF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 MD PACT screen, H2: 20% PEG 3350, 100mM BisTrisPropane pH 8.5, 200mM Na-bromide; tray 233841 f11, BrabA.00113.a at 23 mg/ml, 2.5mM platencin, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.3 46.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.16 α = 90 b = 84.48 β = 120.81 c = 74.02 γ = 90
Symmetry Space Group C 1 2 1
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 RIGAKU SATURN 944+ Rigaku VariMax 2013-02-07 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) 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 1.7 50 98.5 0.033 47.79 11.2 45545 44869 -3 20.929
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 1.7 1.74 96.8 0.187 7.52
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3LRF 1.7 42.28 45545 44869 2264 98.79 0.14382 0.1438 0.1425 0.1555 0.1689 0.1782 RANDOM 16.929
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] -0.06 0.35 -0.1 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.503 r_dihedral_angle_4_deg 16.402 r_dihedral_angle_3_deg 12.637 r_dihedral_angle_1_deg 6.471 r_angle_refined_deg 1.354 r_mcangle_it 1.19 r_angle_other_deg 0.766 r_mcbond_it 0.736 r_mcbond_other 0.734 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.503 r_dihedral_angle_4_deg 16.402 r_dihedral_angle_3_deg 12.637 r_dihedral_angle_1_deg 6.471 r_angle_refined_deg 1.354 r_mcangle_it 1.19 r_angle_other_deg 0.766 r_mcbond_it 0.736 r_mcbond_other 0.734 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3005 Nucleic Acid Atoms Solvent Atoms 433 Heterogen Atoms 31
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction JDirector data collection XDS data reduction