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Crystal structure of lavandulyl diphosphate synthase from Lavandula x intermedia in apo form
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 51.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.357 α = 90 b = 142.085 β = 90 c = 78.666 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 ADSC QUANTUM 315r 2015-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 1.0 NSRRC BL13C1
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 2.15 25 98 0.054 0.064 0.033 11.3 3.5 16659
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 2.15 2.23 93.5 0.418 0.49 0.25 0.855 3.4 1569
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.15 25 15828 814 97.71 0.1819 0.1792 0.1866 0.2341 0.2329 RANDOM 49.902
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] -1.39 4.19 -2.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.435 r_dihedral_angle_4_deg 19.418 r_dihedral_angle_3_deg 19.337 r_dihedral_angle_1_deg 6.082 r_mcangle_it 4.956 r_mcbond_it 3.628 r_mcbond_other 3.587 r_angle_refined_deg 1.825 r_angle_other_deg 0.912 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.435 r_dihedral_angle_4_deg 19.418 r_dihedral_angle_3_deg 19.337 r_dihedral_angle_1_deg 6.082 r_mcangle_it 4.956 r_mcbond_it 3.628 r_mcbond_other 3.587 r_angle_refined_deg 1.825 r_angle_other_deg 0.912 r_chiral_restr 0.129 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1853 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing