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Structure of type II terpene cyclase MstE from Scytonema (apo)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2SQC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 100 mM TRIS, 25% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.18 43.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.46 α = 89.04 b = 48.58 β = 99.97 c = 77.99 γ = 101.86
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 2017-11-04 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 1.95 50 92.2 0.049 9.4 2.3 46089
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 1.95 2.05 92.5 0.549 2
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 2SQC 1.95 30 43775 2304 92.2 0.1749 0.173 0.1871 0.2063 0.2205 RANDOM 43.701
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] 3.51 0.16 1.42 -2.39 0.51 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.045 r_sphericity_free 29.89 r_dihedral_angle_4_deg 16.066 r_dihedral_angle_3_deg 12.534 r_sphericity_bonded 9.272 r_dihedral_angle_1_deg 4.933 r_angle_refined_deg 1.024 r_angle_other_deg 0.893 r_rigid_bond_restr 0.509 r_chiral_restr 0.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.045 r_sphericity_free 29.89 r_dihedral_angle_4_deg 16.066 r_dihedral_angle_3_deg 12.534 r_sphericity_bonded 9.272 r_dihedral_angle_1_deg 4.933 r_angle_refined_deg 1.024 r_angle_other_deg 0.893 r_rigid_bond_restr 0.509 r_chiral_restr 0.057 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5372 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing