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Crystal Structure of Cysteinyl-tRNA Synthetase with Cysteine Substrate Bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LI5 PDB ENTRY 1LI5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 290 16% PEG 8000, 200 MM magnesium acetate, 1MM DTT, cacodylate, 5MM ATP, 10MM cysteine.
100 MM BUFFER, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 290K
Crystal Properties Matthews coefficient Solvent content 2.43 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.98 α = 90 b = 118.98 β = 90 c = 143.84 γ = 90
Symmetry Space Group P 41 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 100 CCD CUSTOM-MADE 2001-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 0.9800 NSLS X12C
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 2.6 55 100 0.091 15.6 8 32383 32373 41.6
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) 2.6 2.74 100 0.52 4.1 8.1 4634
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1LI5 2.6 19.95 32383 32373 3231 99.9 0.251 0.251 0.25 0.2491 0.29 0.289 RANDOM 40.2
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] -0.06 -0.06 0.12
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.2 c_scangle_it 2.46 c_angle_deg 2 c_mcangle_it 1.97 c_scbond_it 1.7 c_improper_angle_d 1.31 c_mcbond_it 1.16 c_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5740 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 16
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling CNS refinement CCP4 data scaling CNS phasing