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T-Muurolol Synthase from Roseiflexus castenholzii (TmS) in complex with converted 6,7-DHFPP (compound 3+)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9HQI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1 M MES; 0.05 M MgCl2; 15% PEG 400
Crystal Properties Matthews coefficient Solvent content 3.98 69.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.37 α = 90 b = 132.37 β = 90 c = 129.99 γ = 90
Symmetry Space Group P 43 21 2
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 2023-06-03 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 2.1 30 99.4 0.096 10.9 5 67327
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 2.1 2.2 100 0.688 2.8 5.4
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 2.1 30 63936 3365 99.36 0.15392 0.15186 0.1629 0.19216 0.1963 RANDOM 40.433
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] -1.53 -1.53 3.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.547 r_dihedral_angle_4_deg 15.277 r_dihedral_angle_3_deg 13.141 r_long_range_B_refined 5.921 r_long_range_B_other 5.704 r_scangle_other 4.885 r_dihedral_angle_1_deg 4.726 r_mcangle_it 4.278 r_mcangle_other 4.277 r_scbond_it 3.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.547 r_dihedral_angle_4_deg 15.277 r_dihedral_angle_3_deg 13.141 r_long_range_B_refined 5.921 r_long_range_B_other 5.704 r_scangle_other 4.885 r_dihedral_angle_1_deg 4.726 r_mcangle_it 4.278 r_mcangle_other 4.277 r_scbond_it 3.826 r_scbond_other 3.826 r_mcbond_it 3.184 r_mcbond_other 3.181 r_angle_other_deg 1.277 r_angle_refined_deg 1.267 r_rigid_bond_restr 1.179 r_chiral_restr 0.063 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4957 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing