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Crystal Structure of Acetoacetyl-CoA Reductase from Burkholderia Pseudomallei 1710b with bound NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EZL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 BupsA.00010.e.A1.PS00061 at 19.3 mg/ml incubated with 4 mM NADP, mixed 1:1 with Morpheus(c8): 12.5% (w/v) PEG-1000, 12.5% (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M MOPS/ HEPES-Na, pH = 7.5, 0.03 M each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate, crystals were soaked for 24 hours with 5 mM NADP in well solution, harvested directly
Crystal Properties Matthews coefficient Solvent content 2.18 43.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.31 α = 90 b = 66.31 β = 90 c = 115.26 γ = 90
Symmetry Space Group P 42 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 100 CCD RIGAKU SATURN 944+ 2017-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 50 99.5 0.062 0.999 22.03 8.9 28909 15.87
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 93.2 0.458 0.856 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3EZL 1.7 46.888 1.35 28908 2030 99.46 0.1461 0.1443 0.1461 0.1709 0.1727 19.0649
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.162 f_angle_d 0.772 f_chiral_restr 0.054 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1842 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 56
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHENIX phasing