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Human putative tRNA(1-methyladenosine)methyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I9G PDB Entry 1I9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 11 % PEG3350, 0.2M lithium citrate, 0.1M BisTris, 10% PEG400, pH 6.5, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.533 α = 90 b = 157.106 β = 90 c = 113.492 γ = 90
Symmetry Space Group C 2 2 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 210 2005-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F2 0.97914 CHESS F2
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 2.3 78.57 99.6 0.082 5.7 30305
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 100 5.9
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB Entry 1I9G 2.5 78.567 23535 744 98.978 0.248 0.2466 0.2471 0.2822 0.246 thin shells 44.301
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] 3.107 -2.692 -0.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.114 r_dihedral_angle_3_deg 15.738 r_dihedral_angle_4_deg 13.264 r_dihedral_angle_1_deg 6.291 r_mcangle_it 3.522 r_scangle_it 3.057 r_mcbond_it 2.277 r_scbond_it 2.261 r_angle_refined_deg 1.366 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.114 r_dihedral_angle_3_deg 15.738 r_dihedral_angle_4_deg 13.264 r_dihedral_angle_1_deg 6.291 r_mcangle_it 3.522 r_scangle_it 3.057 r_mcbond_it 2.277 r_scbond_it 2.261 r_angle_refined_deg 1.366 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.23 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.083 r_symmetry_hbond_refined 0.077 r_bond_refined_d 0.017 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3779 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 56
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction