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Crystal structure of lavandulyl diphosphate synthase from Lavandula x intermedia in complex with S-thiolo-isopentenyldiphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V7U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 Ammonium Sulfate, Glycerol, PEG400
Crystal Properties Matthews coefficient Solvent content 2.55 51.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.392 α = 90 b = 141.606 β = 90 c = 78.918 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 RAYONIX MX-300 2015-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.05 25 98.9 0.056 0.066 0.035 9.8 3.5 19241
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.12 93.4 0.42 0.498 0.265 0.853 3.3 1783
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1V7U 2.05 25 18346 879 98.59 0.1707 0.1685 0.1806 0.2144 0.2206 RANDOM 44.861
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] -2.21 4.31 -2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.086 r_dihedral_angle_4_deg 23.124 r_dihedral_angle_3_deg 16.593 r_dihedral_angle_1_deg 6.413 r_mcangle_it 4.788 r_mcbond_it 3.569 r_mcbond_other 3.568 r_angle_refined_deg 2.077 r_angle_other_deg 1.003 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.086 r_dihedral_angle_4_deg 23.124 r_dihedral_angle_3_deg 16.593 r_dihedral_angle_1_deg 6.413 r_mcangle_it 4.788 r_mcbond_it 3.569 r_mcbond_other 3.568 r_angle_refined_deg 2.077 r_angle_other_deg 1.003 r_chiral_restr 0.132 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1853 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing