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Crystal structure of diterpene synthase VenA from Streptomyces venezuelae ATCC 15439 in complex with pyrophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TBD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 25% PEG SMEAR MEDIUM; 0.1M HEPES; pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.42 49.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.789 α = 90 b = 92.789 β = 90 c = 81.048 γ = 120
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 Bruker PHOTON III 2021-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.34138
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.18 36.02 99.9 0.0652 10.43 4.49 40733
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 2.18 2.21 100 0.4139 2.07 3.44
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 6TBD 2.18 36.02 36822 2077 95.49 0.1783 0.1749 0.1819 0.238 0.2376 RANDOM 40.118
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] 0.09 0.05 0.09 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.234 r_dihedral_angle_4_deg 19.215 r_dihedral_angle_3_deg 15.115 r_dihedral_angle_1_deg 5.911 r_angle_refined_deg 1.464 r_angle_other_deg 1.311 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.234 r_dihedral_angle_4_deg 19.215 r_dihedral_angle_3_deg 15.115 r_dihedral_angle_1_deg 5.911 r_angle_refined_deg 1.464 r_angle_other_deg 1.311 r_chiral_restr 0.072 r_bond_refined_d 0.008 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 5161 Nucleic Acid Atoms Solvent Atoms 462 Heterogen Atoms 118
Software Software Software Name Purpose SAINT data reduction SAINT data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing