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Crystal structure of a tRNA-guanine-N1-methyltransferase from Mycobacterium abscessus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KNU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 MyabA.00937.a.A1 PW30232 at 24.4 mg/mL against JCSG + E1, 2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5 with 20% ethylene glycol as a cryo-protectant, crystal tracking ID 219633e1, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.36 47.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.66 α = 90 b = 79.08 β = 90 c = 86.01 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 CCD ADSC QUANTUM 315r 2011-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97946 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 50 98.5 0.045 27.52 6.5 55952 55136 -3 27.064
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 1.7 1.74 97.6 0.495 3.78 6.6 4112
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 3knu 1.7 50 54992 2798 98.29 0.1723 0.1709 0.174 0.1975 0.2001 RANDOM 21.637
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] -0.54 -0.22 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.659 r_dihedral_angle_4_deg 17.194 r_dihedral_angle_3_deg 12.437 r_dihedral_angle_1_deg 5.433 r_scangle_it 3.976 r_scbond_it 2.419 r_mcangle_it 1.629 r_angle_refined_deg 1.448 r_mcbond_it 0.912 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.659 r_dihedral_angle_4_deg 17.194 r_dihedral_angle_3_deg 12.437 r_dihedral_angle_1_deg 5.433 r_scangle_it 3.976 r_scbond_it 2.419 r_mcangle_it 1.629 r_angle_refined_deg 1.448 r_mcbond_it 0.912 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3352 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 16
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction