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The complex structure of aTrm5 and tRNACys
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZZM PDB ENTRY 2ZZM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop, vapor diffusion 7.5 293 87.5mM Mg(HCOO)2, 4.38% PEG 3350, 43.8mM CH3COONa pH 4.6, 8.8% MPD, 0.4mM CYMAL-5, 12.5mM Na-HEPES pH 7.5, sitting drop, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 46.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.838 α = 90 b = 106.537 β = 90 c = 134.459 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 2007-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.95 50 25625 -0.1
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 ENTRY 2ZZM 2.95 46.69 25384 1295 99.9 0.226 0.226 0.2265 0.295 0.2987 RANDOM 72.6
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] 0.91 -16.87 15.96
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 2.89 c_mcangle_it 2.3 c_scbond_it 1.76 c_mcbond_it 1.31 c_angle_deg 1.3 c_improper_angle_d 1.21 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 2.89 c_mcangle_it 2.3 c_scbond_it 1.76 c_mcbond_it 1.31 c_angle_deg 1.3 c_improper_angle_d 1.21 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5486 Nucleic Acid Atoms 3034 Solvent Atoms 25 Heterogen Atoms 61
Software Software Software Name Purpose CNS refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing