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Crystal structure of Pyrrolysyl-tRNA synthetase from Desulfitobacterium hafniense
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other PylS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 50mM Na cacodylate, 50mM Ammonium sulfate, 20% PEG400, 10mM Na acetate, 0.2mM Na formate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.34 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.925 α = 90 b = 128.555 β = 90 c = 124.241 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 315 mirrors 2007-05-30 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) 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 2.5 50 100 0.076 55.82 14.5 35020 35020 32.8
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 PylS 2.5 44.67 34900 1768 100 0.214 0.214 0.2136 0.275 0.2752 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] -7.64 -4.92 12.55
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.8 c_scangle_it 2.57 c_mcangle_it 2.31 c_scbond_it 1.61 c_mcbond_it 1.32 c_angle_deg 1.3 c_improper_angle_d 0.78 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.8 c_scangle_it 2.57 c_mcangle_it 2.31 c_scbond_it 1.61 c_mcbond_it 1.32 c_angle_deg 1.3 c_improper_angle_d 0.78 c_bond_d 0.007 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 6773 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing