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Crystal structure of 1,8-cineole synthase from Streptomyces clavuligerus in complex with 2-fluoroneryl diphosphate and 2-fluorogeranyl diphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PS1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 90 mM LiNaK (0.3 M Lithium sulfate, 0.3 M Sodium sulfate, 0.3 M Potassium sulfate), 0.1 M Buffer System 5 (BES, Triethanolamine) pH 7.5, 50 % v/v Precipitant Mix 8 (10% w/v PEG 20000, 50% w/v Trimethyl propane, 2% w/v NDSB 195)
Crystal Properties Matthews coefficient Solvent content 3.07 59.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.745 α = 92.67 b = 60.826 β = 89.98 c = 64.258 γ = 101.77
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2017-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.506 64.19 95.9 0.035 0.032 10 2 136704
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 1.51 1.53 93.4 0.315 2.1 2
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 1PS1 1.51 43.42 1.99 136690 7052 95.9 0.151 0.149 0.1609 0.174 0.185
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 10.655 f_angle_d 0.956 f_chiral_restr 0.051 f_bond_d 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4950 Nucleic Acid Atoms Solvent Atoms 822 Heterogen Atoms 128
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing