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Crystal structure of Archaeoglobus fulgidus O-phosphoseryl-tRNA synthetase E418N/E420N mutant complexed with tRNAAmber and O-phosphoserine ("amber complex")
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DU3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 8% PEG 6000, 1.2M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.33 63.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.323 α = 90 b = 148.323 β = 90 c = 152.617 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 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 1.00 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 3.3 50 99.8 29647 29582
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.3 3.42 99.6
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 2DU3 3.3 49.14 29582 1458 99.7 0.265 0.265 0.2278 0.329 0.2816 RANDOM 104.2
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] -5.92 9.62 -5.92 11.84
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 c_scangle_it 15.98 c_mcangle_it 14.18 c_scbond_it 12.02 c_mcbond_it 9.37 c_angle_deg 1.1 c_improper_angle_d 0.95 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 c_scangle_it 15.98 c_mcangle_it 14.18 c_scbond_it 12.02 c_mcbond_it 9.37 c_angle_deg 1.1 c_improper_angle_d 0.95 c_bond_d 0.005 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 8080 Nucleic Acid Atoms 1517 Solvent Atoms Heterogen Atoms 22
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing