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tRNA (N1G37) Methyltransferase (TrmD) of Mycobacterium avium complexed with S-Adenosyl homocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZHJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 0.2 M sodium sulfate, 0.1M bis-tris propane, pH 8.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.86 56.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.972 α = 90 b = 70.972 β = 90 c = 240.161 γ = 90
Symmetry Space Group P 43 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 2020-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92010 NSLS-II 17-ID-1
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 1.752 61.098 91.6 0.1568 0.1651 0.0505 0.998 9.95 10.66 28202
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.752 2.018 72.3 1.6408 1.7068 0.465 0.709 1.7 13.24 1410
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 1.752 61.1 28202 1441 44.8 0.22 0.2189 0.2062 0.2389 0.2299 RANDOM 31.32
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] -0.2387 -0.2387 0.4774
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.25 t_omega_torsion 3.28 t_angle_deg 0.85 t_bond_d 0.009 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2992 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 52
Software Software Software Name Purpose BUSTER refinement autoPROC data processing XDS data reduction Aimless data scaling STARANISO data scaling PHENIX phasing