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Crystal structure of seryl-tRNA synthetase from Pyrococcus horikoshii complexed with ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DQ0 PDB ENTRY 2dq0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 1.6M ammonium sulfate, 0.1M magnesium acetate, 0.1M Hepes-NaOH pH 7.5, 2mM ATP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.46 64.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.656 α = 90 b = 120.499 β = 90 c = 126.777 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 90 CCD ADSC QUANTUM 315 2005-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.8 50 99.8 0.062 0.062 32.3 7.4 37276 37201 -3 101.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.9 99.7 0.612 0.612 3.2 7.4 3657
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-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 2dq0 2.8 48.52 37143 37085 1870 99.8 0.192 0.1897 0.251 0.2472 RANDOM 64.4
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] 9.91 -13.97 4.05
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.7 c_scangle_it 8.9 c_scbond_it 6.79 c_mcangle_it 5.96 c_mcbond_it 4.13 c_angle_deg 1.58 c_improper_angle_d 1.32 c_bond_d 0.0092 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.7 c_scangle_it 8.9 c_scbond_it 6.79 c_mcangle_it 5.96 c_mcbond_it 4.13 c_angle_deg 1.58 c_improper_angle_d 1.32 c_bond_d 0.0092 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 7398 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 81
Software Software Software Name Purpose CNS refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing