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Crystal structure of TnmS3 in complex with TNM C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UPM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 5.5 298 100 mM ammonium acetate, 100 mM bis-Tris, and 17% w/v polyethylene glycol 3350.
Crystal Properties Matthews coefficient Solvent content 2.08 40.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.31 α = 90 b = 67.76 β = 90 c = 83.91 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2017-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 45.31 96.3 0.17 0.98 6.9 4.7 12754
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 82.4 0.837 0.525 1.9 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5UPM 2.2 45.31 12754 695 97.9 0.21837 0.21605 0.2206 0.26042 0.263 RANDOM 22.694
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] 1.26 -0.39 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.076 r_dihedral_angle_3_deg 14.785 r_dihedral_angle_4_deg 12.02 r_dihedral_angle_1_deg 6.487 r_long_range_B_refined 4.494 r_long_range_B_other 4.494 r_scangle_other 2.627 r_mcangle_it 2.143 r_mcangle_other 2.142 r_angle_refined_deg 1.937
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.076 r_dihedral_angle_3_deg 14.785 r_dihedral_angle_4_deg 12.02 r_dihedral_angle_1_deg 6.487 r_long_range_B_refined 4.494 r_long_range_B_other 4.494 r_scangle_other 2.627 r_mcangle_it 2.143 r_mcangle_other 2.142 r_angle_refined_deg 1.937 r_scbond_it 1.569 r_scbond_other 1.569 r_mcbond_it 1.271 r_mcbond_other 1.27 r_angle_other_deg 1.024 r_chiral_restr 0.344 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 1856 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection SCALA data scaling MOLREP phasing MOSFLM data reduction