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Crystal structure of TnmH in complex with SAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CLW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.2 M L-Proline, 0.1 M HEPES, pH 7.5, 10% w/v Polyethlene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.79 55.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.22 α = 90 b = 116.22 β = 90 c = 110.4 γ = 120
Symmetry Space Group P 31 2 1
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 2017-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.73 55.24 100 0.148 0.173 0.088 0.995 10.4 7 23384
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.73 2.88 0.871 1.037 0.554 0.58
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 6CLW 2.73 55.24 22188 1133 99.95 0.22793 0.22534 0.2287 0.2778 0.2762 RANDOM 59.805
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] 0.83 0.41 0.83 -2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.131 r_dihedral_angle_3_deg 18.6 r_dihedral_angle_4_deg 17.169 r_dihedral_angle_1_deg 6.832 r_long_range_B_refined 5.641 r_long_range_B_other 5.641 r_mcangle_it 3.091 r_mcangle_other 3.091 r_scangle_other 3.002 r_mcbond_it 1.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.131 r_dihedral_angle_3_deg 18.6 r_dihedral_angle_4_deg 17.169 r_dihedral_angle_1_deg 6.832 r_long_range_B_refined 5.641 r_long_range_B_other 5.641 r_mcangle_it 3.091 r_mcangle_other 3.091 r_scangle_other 3.002 r_mcbond_it 1.807 r_mcbond_other 1.807 r_scbond_it 1.77 r_scbond_other 1.769 r_angle_refined_deg 1.354 r_angle_other_deg 0.974 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5077 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing