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T-Muurolol Synthase from Roseiflexus castenholzii (TmS) in complex with FSPP
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 7 277 0.1 M HEPES; 0.05 mM MgCl2; 30% Jeffamine ED-2001
Crystal Properties Matthews coefficient Solvent content 3.82 67.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.61 α = 90 b = 131.61 β = 90 c = 126.16 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 2024-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.45 30 97 0.086 16.1 9.4 40087
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 2.45 2.45 98.5 0.777 2.6 9.7
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 2.45 30 38053 2003 96.97 0.20696 0.20443 0.2093 0.25633 0.2556 RANDOM 67.144
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] 0.21 0.21 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.547 r_dihedral_angle_4_deg 14.668 r_dihedral_angle_3_deg 14.304 r_dihedral_angle_1_deg 4.155 r_long_range_B_refined 3.042 r_long_range_B_other 3.042 r_mcangle_it 2.085 r_mcangle_other 2.085 r_scangle_other 1.999 r_mcbond_it 1.436
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.547 r_dihedral_angle_4_deg 14.668 r_dihedral_angle_3_deg 14.304 r_dihedral_angle_1_deg 4.155 r_long_range_B_refined 3.042 r_long_range_B_other 3.042 r_mcangle_it 2.085 r_mcangle_other 2.085 r_scangle_other 1.999 r_mcbond_it 1.436 r_mcbond_other 1.436 r_scbond_it 1.386 r_scbond_other 1.385 r_angle_refined_deg 1.13 r_angle_other_deg 1.046 r_rigid_bond_restr 0.258 r_chiral_restr 0.033 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 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 4940 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing