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T-Muurolol Synthase from Roseiflexus castenholzii (TmS) in complex with 2,3-DHFPP [P2(1)2(1)2(1)]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.1 M Tris; 0.05 M MgCl2; 25% PEG 1000
Crystal Properties Matthews coefficient Solvent content 1.98 37.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.43 α = 90 b = 75.13 β = 90 c = 134.18 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 2022-09-10 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 1.8 30 98.1 0.059 12.4 4.1 56395
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 1.8 1.9 99.8 0.679 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 30 53506 2816 98.08 0.1846 0.1826 0.1926 0.2193 0.2285 RANDOM 39.232
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] 2.02 0.7 -2.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.145 r_dihedral_angle_4_deg 15.68 r_dihedral_angle_3_deg 14.314 r_dihedral_angle_1_deg 4.813 r_angle_refined_deg 1.159 r_angle_other_deg 1.157 r_rigid_bond_restr 0.578 r_chiral_restr 0.049 r_gen_planes_refined 0.003 r_bond_refined_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.145 r_dihedral_angle_4_deg 15.68 r_dihedral_angle_3_deg 14.314 r_dihedral_angle_1_deg 4.813 r_angle_refined_deg 1.159 r_angle_other_deg 1.157 r_rigid_bond_restr 0.578 r_chiral_restr 0.049 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4827 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing