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MYCOBACTERIUM ABSCESSUS TRNA METHYLTRANSFERASE IN APO FORM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NVR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2ul protein at concentration 24mg/ml, and 2ul buffer (0.1 M sodium cacodylate, 2 M ammonium sulfate pH 6.5),
1uL 50% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.69 54.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.785 α = 90 b = 79.375 β = 90 c = 86.604 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 PIXEL DECTRIS EIGER X 9M 2019-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92 NSLS-II 17-ID-1
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 1.87 29.26 99 0.062 0.999 16 6.6 42678 0.054 0.656
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.91 86.7 0.612 1.1 5.8
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 6NVR 1.87 29.26 40498 2116 98.93 0.17688 0.17418 0.1812 0.22625 0.2289 RANDOM 37.328
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.365 r_dihedral_angle_4_deg 16.559 r_long_range_B_refined 16.255 r_long_range_B_other 15.844 r_dihedral_angle_3_deg 13.026 r_dihedral_angle_1_deg 6.686 r_scangle_other 6.265 r_mcangle_it 4.37 r_mcangle_other 4.37 r_scbond_it 4.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.365 r_dihedral_angle_4_deg 16.559 r_long_range_B_refined 16.255 r_long_range_B_other 15.844 r_dihedral_angle_3_deg 13.026 r_dihedral_angle_1_deg 6.686 r_scangle_other 6.265 r_mcangle_it 4.37 r_mcangle_other 4.37 r_scbond_it 4.152 r_scbond_other 4.151 r_mcbond_it 3.086 r_mcbond_other 3.074 r_angle_refined_deg 1.576 r_angle_other_deg 1.368 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 3300 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing