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Structure of type II terpene cyclase MstE from Scytonema in complex with farnesyl dihydroxybenzoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SBB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 100 mM HEPES, 4 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.08 40.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.98 α = 90 b = 77.42 β = 90 c = 90.91 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER X 16M 2018-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 1.35 50 95.9 0.041 15.7 3.8 72004
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.45 2.6
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 6SBB 1.35 15 68352 3598 95.8 0.1173 0.1154 0.1112 0.1531 0.1529 RANDOM 18.347
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] 3.65 -0.61 -3.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.49 r_dihedral_angle_4_deg 16.01 r_dihedral_angle_3_deg 11.926 r_rigid_bond_restr 5.61 r_dihedral_angle_1_deg 5.508 r_angle_refined_deg 1.852 r_angle_other_deg 1.783 r_chiral_restr 0.116 r_bond_refined_d 0.014 r_gen_planes_refined 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.49 r_dihedral_angle_4_deg 16.01 r_dihedral_angle_3_deg 11.926 r_rigid_bond_restr 5.61 r_dihedral_angle_1_deg 5.508 r_angle_refined_deg 1.852 r_angle_other_deg 1.783 r_chiral_restr 0.116 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2758 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing