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Crystal structure of an enoyl-(acyl carrier protein) reductase from Bartonella henselae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GRK PDB ENTRY 3grk
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 BaheA.00010.b.A1 PW26981 selenomethionine-labeled at 27.5 mg/mL against PACT screen condition B5, 0.1 M MIB pH 8.0, 25% PEG 1500 with 15% ethylene glycol as cryo-protectant, crystal tracking ID 232038b5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.13 42.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.36 α = 90 b = 76.86 β = 107.99 c = 171.95 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 MARMOSAIC 300 mm CCD 2012-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07806 APS 21-ID-D
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 2.4 50 99.1 0.089 10.42 3.8 59634 59084 -3 44.808
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 2.4 2.46 98.6 0.441 3.14
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 3grk 2.4 50 59083 2994 99.13 0.1972 0.1956 0.1888 0.2262 0.2199 RANDOM 37.2283
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] 0.14 -1.21 0.79 -1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.691 r_dihedral_angle_4_deg 16.216 r_dihedral_angle_3_deg 13.094 r_dihedral_angle_1_deg 5.554 r_angle_refined_deg 1.484 r_angle_other_deg 1.349 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.691 r_dihedral_angle_4_deg 16.216 r_dihedral_angle_3_deg 13.094 r_dihedral_angle_1_deg 5.554 r_angle_refined_deg 1.484 r_angle_other_deg 1.349 r_chiral_restr 0.082 r_bond_refined_d 0.012 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 10961 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction