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Crystal structure of tRNA (m1A58) methyltransferase TrmI from Aquifex aeolicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O54 PDB code: 1O54
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 293 0.1M Tris, 20% Ethanol, pH8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.14 60.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.826 α = 90 b = 97.237 β = 90 c = 212.687 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 315 2006-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.2 50 96.7 0.075 6.6 72044
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 77 0.256 3.6
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 PDB code: 1O54 2.2 49.75 68373 3597 96.75 0.19557 0.19376 0.189 0.22964 0.2243 RANDOM 27.189
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] -0.07 0.1 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.826 r_dihedral_angle_3_deg 15.306 r_dihedral_angle_4_deg 13.501 r_dihedral_angle_1_deg 5.947 r_scangle_it 2.595 r_mcangle_it 2.383 r_scbond_it 1.698 r_mcbond_it 1.592 r_angle_refined_deg 1.107 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.826 r_dihedral_angle_3_deg 15.306 r_dihedral_angle_4_deg 13.501 r_dihedral_angle_1_deg 5.947 r_scangle_it 2.595 r_mcangle_it 2.383 r_scbond_it 1.698 r_mcbond_it 1.592 r_angle_refined_deg 1.107 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.202 r_nbd_refined 0.18 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8092 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing