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T-Muurolol Synthase from Roseiflexus castenholzii (TmS) in complex with 2,3-DHFPP [P4(3)2(1)2(1)]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9HQD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.1 M TRIS, 0.05 mM MgCl2, 25% PEG 1000
Crystal Properties Matthews coefficient Solvent content 3.9 68.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.81 α = 90 b = 131.81 β = 90 c = 128.43 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 2022-12-01 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 96.6 0.058 13.3 3.8 64130
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 97.9 0.595 2 3.5
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 60902 3206 96.56 0.17206 0.17044 0.1818 0.20136 0.2112 RANDOM 44.143
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] -0.35 -0.35 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.597 r_dihedral_angle_4_deg 15.402 r_dihedral_angle_3_deg 13.766 r_dihedral_angle_1_deg 4.431 r_long_range_B_refined 4.197 r_long_range_B_other 4.046 r_scangle_other 3.109 r_mcangle_it 3.046 r_mcangle_other 3.045 r_scbond_it 2.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.597 r_dihedral_angle_4_deg 15.402 r_dihedral_angle_3_deg 13.766 r_dihedral_angle_1_deg 4.431 r_long_range_B_refined 4.197 r_long_range_B_other 4.046 r_scangle_other 3.109 r_mcangle_it 3.046 r_mcangle_other 3.045 r_scbond_it 2.317 r_scbond_other 2.317 r_mcbond_it 2.16 r_mcbond_other 2.16 r_angle_other_deg 1.153 r_angle_refined_deg 1.152 r_rigid_bond_restr 0.688 r_chiral_restr 0.05 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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 4939 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement XDS data reduction PROCOR data scaling PHASER phasing