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Crystal Structure of a 3-oxoacyl-[acyl-carrier protein] Reductase with bound NAD from Brucella melitensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NBR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 BrmeB.00010.f.B1.PS01889 at 17.41 mg/ml, incubated with 4mM NAD, mixed 1:1 with an equal volume MCSG1(a1): 20% (w/v) PEG-8000, 0.1 M HEPES/NaOH, pH=7.5, cryoprotected with 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.37 48.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.07 α = 90 b = 105.62 β = 90 c = 126.04 γ = 90
Symmetry Space Group C 2 2 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 300 mm CCD Beryllium Lenses 2016-04-20 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) Rrim I (All) 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 1.55 35 99.3 0.073 0.081 0.998 14.53 79835 -3 12.72
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 1.55 1.59 98.1 0.524 0.829 2.93 4.5
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 4NBR 1.55 34.68 1.35 79815 1906 99.27 0.1466 0.1461 0.147 0.1695 0.1696 17.6239
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 11.426 f_angle_d 0.814 f_chiral_restr 0.054 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3860 Nucleic Acid Atoms Solvent Atoms 570 Heterogen Atoms 163
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MOLREP phasing