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X-ray crystal structure of a putative Acetoacetyl-CoA reductase from Burkholderia cenocepacia bound to the co-factor NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K6C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 JCSG+ G4: 0.1 M TRIS-HCl, 200 mM trimethylamine N-oxide, 20% PEG 2000 MME , pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.07 40.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.74 α = 90 b = 101.33 β = 90 c = 134.56 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 MARMOSAIC 225 mm CCD 2013-04-03 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) 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 1.5 47.415 99.1 0.063 19.78 146320 145003 -3 19.215
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 1.5 1.54 98.4 0.546 3.71
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4K6C 1.5 47.46 146320 137740 7264 99.13 0.1676 0.1652 0.2126 0.2053 RANDOM 15.131
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] -0.12 -0.38 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.024 r_sphericity_free 32.668 r_dihedral_angle_4_deg 11.216 r_dihedral_angle_3_deg 10.982 r_sphericity_bonded 7.913 r_dihedral_angle_1_deg 5.627 r_rigid_bond_restr 2.062 r_mcangle_it 1.859 r_mcbond_it 1.572 r_mcbond_other 1.572
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.024 r_sphericity_free 32.668 r_dihedral_angle_4_deg 11.216 r_dihedral_angle_3_deg 10.982 r_sphericity_bonded 7.913 r_dihedral_angle_1_deg 5.627 r_rigid_bond_restr 2.062 r_mcangle_it 1.859 r_mcbond_it 1.572 r_mcbond_other 1.572 r_angle_refined_deg 1.409 r_angle_other_deg 0.811 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7152 Nucleic Acid Atoms Solvent Atoms 945 Heterogen Atoms 118
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction