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The structure of SenA in complex with N,N,N-trimethyl-histidine and thioglucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X8B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 291 20% PEG 6000, 0.1 M Tris/HCl pH 8.0, 0.2 M ammonium chloride
Crystal Properties Matthews coefficient Solvent content 2.16 43.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.641 α = 90 b = 95.895 β = 90 c = 61.846 γ = 90
Symmetry Space Group P 21 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 Bruker PHOTON III 2023-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.34138
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 1.92 33.2 99.7 0.0792 12.65 5.07 31836
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 1.92 1.95 97.4 0.2694 3.31 3.69
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 1.92 33.2 30170 1580 99.59 0.16758 0.16506 0.1757 0.21434 0.2239 RANDOM 22.864
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] -1.51 0.65 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.686 r_dihedral_angle_4_deg 16.81 r_dihedral_angle_3_deg 14.547 r_dihedral_angle_1_deg 7.152 r_long_range_B_refined 5.564 r_long_range_B_other 5.36 r_scangle_other 3.443 r_mcangle_it 2.779 r_mcangle_other 2.778 r_scbond_it 2.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.686 r_dihedral_angle_4_deg 16.81 r_dihedral_angle_3_deg 14.547 r_dihedral_angle_1_deg 7.152 r_long_range_B_refined 5.564 r_long_range_B_other 5.36 r_scangle_other 3.443 r_mcangle_it 2.779 r_mcangle_other 2.778 r_scbond_it 2.215 r_scbond_other 2.215 r_mcbond_it 1.865 r_mcbond_other 1.865 r_angle_refined_deg 1.539 r_angle_other_deg 1.379 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3137 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement SAINT data scaling SAINT data reduction PHASER phasing PDB_EXTRACT data extraction