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Crystal Structure of Class IB terpene synthase bound with geranylcitronellyl diphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YO8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.3 298 PEG3350, Ammonium Acetate, Magnesium Chloride, Methanol
Crystal Properties Matthews coefficient Solvent content 2.16 43.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.87 α = 94.63 b = 53.48 β = 104.72 c = 76.54 γ = 113.33
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 MX225HE 2018-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.99 48.12 97.8 0.095 0.11 0.998 13.65 3.905 47141 34.108
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.04 96.6 0.842 0.978 0.532 2 3.93
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 5yo8 1.99 48.12 44802 2339 97.88 0.1813 0.179 0.1836 0.2246 0.2297 RANDOM 32.585
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] 1.49 0.76 -0.11 -0.93 0.28 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.355 r_dihedral_angle_4_deg 17.032 r_dihedral_angle_3_deg 14.514 r_dihedral_angle_1_deg 5.663 r_angle_refined_deg 1.32 r_angle_other_deg 1.281 r_chiral_restr 0.072 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.355 r_dihedral_angle_4_deg 17.032 r_dihedral_angle_3_deg 14.514 r_dihedral_angle_1_deg 5.663 r_angle_refined_deg 1.32 r_angle_other_deg 1.281 r_chiral_restr 0.072 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5767 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 116
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing