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The structure of SenA in complex with N,N,N-trimethyl-histidine
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 2.2 44.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.986 α = 90 b = 96.355 β = 90 c = 62.338 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 DECTRIS EIGER X 9M 2023-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1.0 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.3 22.48 94.7 0.04 0.045 0.02 0.997 30.4 4.4 97669
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 1.3 1.35 86.8 0.137 9.1 4.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.3 22.48 92661 4915 94.38 0.12399 0.12238 0.15499 0.1842 RANDOM 18.021
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] -0.25 0.26 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.271 r_dihedral_angle_4_deg 17.56 r_dihedral_angle_3_deg 12.978 r_dihedral_angle_1_deg 6.812 r_rigid_bond_restr 5.335 r_long_range_B_refined 4.64 r_long_range_B_other 4.523 r_scangle_other 4.493 r_scbond_it 3.939 r_scbond_other 3.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.271 r_dihedral_angle_4_deg 17.56 r_dihedral_angle_3_deg 12.978 r_dihedral_angle_1_deg 6.812 r_rigid_bond_restr 5.335 r_long_range_B_refined 4.64 r_long_range_B_other 4.523 r_scangle_other 4.493 r_scbond_it 3.939 r_scbond_other 3.938 r_mcangle_it 3.106 r_mcangle_other 3.105 r_mcbond_it 3.071 r_mcbond_other 3.071 r_angle_refined_deg 2.139 r_angle_other_deg 1.62 r_chiral_restr 0.136 r_bond_refined_d 0.019 r_gen_planes_refined 0.015 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 3207 Nucleic Acid Atoms Solvent Atoms 621 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing