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Crystal structure of Isosesquilavandulyl Diphosphate Synthase from Streptomyces sp. strain CNH-189 in complex with DMAPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XK3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 PROTEIN: 10 mg/mL in 25 mM Tris-Cl (pH 7.5) and 150 mM NaCl
RESERVOIR: 0.2 M (NH4)2SO4, 0.1 M MES pH 6.5, 30% PEG 5000MME
SOAK: 5 mM MgCl2, 5 mM (NH4)4P2O7, 0.1 M MES pH 6.5, 30% PEG 5000MME, 10 mM DMAPP
Crystal Properties Matthews coefficient Solvent content 2.42 49.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.924 α = 90 b = 120.653 β = 90 c = 126.327 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 RAYONIX MX-300 2017-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0000 NSRRC BL15A1
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 1.91 25 98.5 0.048 0.998 27.8 3.2 79758
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 1.91 1.98 97.1 0.459 0.958 2.7 3.3
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5XK3 1.911 24.729 1.35 79708 1999 98.4 0.1694 0.1688 0.1691 0.1921 0.1935 RANDOM
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 21.007 f_angle_d 0.754 f_chiral_restr 0.046 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6842 Nucleic Acid Atoms Solvent Atoms 904 Heterogen Atoms 149
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling