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Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruiginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 MgCl2, CaCl2, PEG MME 550, PEG 20000, MOPS/Na-HEPES pH7.5
Crystal Properties Matthews coefficient Solvent content 3 58.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.796 α = 90 b = 59.796 β = 90 c = 124.18 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 110 CCD ADSC QUANTUM 315 toroidal focusing mirror 2015-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 1.0 NSRRC BL13C1
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 1.62 30.03 95.4 0.06 19 9.9 29132 18.25
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 1.62 1.65 71.5 0.73 3.9 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 4CND 1.62 29.58 27532 1403 93.4 0.179 0.178 0.1786 0.204 0.2002 RANDOM 20.8
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] -0.061 -0.061 0.122
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.47 t_omega_torsion 3.37 t_angle_deg 1.02 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.47 t_omega_torsion 3.37 t_angle_deg 1.02 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1295 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement MOSFLM data reduction SCALEPACK data scaling MOLREP phasing