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Crystal structure of Pyrococcus horikoshii quinolinate synthase (NadA) with bound L-malate and Fe4S4 cluster
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KTN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 210 mM ammonium chloride, 8 - 15% polyethylene glycol 4000, and 40 mM HEPES, pH 5.5 - 7.5. L-malic acid, pH 5.6, was added to the protein solution to a final concentration of 10 mM
Crystal Properties Matthews coefficient Solvent content 2.08 40.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.333 α = 90 b = 54.639 β = 90.79 c = 55.613 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315 2013-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97925 APS 24-ID-E
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 35 97.3 0.046 15.9 2.9 44361
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 1.55 99.9 0.484 2.7 2.8
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 5KTN 1.5 29.943 1.35 44346 2271 97.19 0.1485 0.1462 0.1461 0.1926 0.1928
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 14.585 f_angle_d 1.846 f_chiral_restr 0.077 f_bond_d 0.011 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2359 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement PHENIX phasing HKL-2000 data reduction HKL-2000 data scaling