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Crystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus bound to cysteine sulfamoyl adenylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H3N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Tris, Beta-Mercaptoethanol, MgCl2, NaCl, Cysteine sulfamoyl adenylate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.54 72.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.75 α = 90 b = 143.75 β = 90 c = 163.89 γ = 120
Symmetry Space Group P 65 2 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 SBC-2 2002-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97903 APS 19-ID
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 2.55 50 99.9 0.061 48.9 14.8 33228 33200 -3 57.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.64 100 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MOLECULAR REPLACEMENT THROUGHOUT 2.55 50 33186 29801 2957 89.8 0.225 0.225 0.225 0.2223 0.257 0.2514 RANDOM 72.9
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] 0.84 5.99 0.84 -1.68
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_scangle_it 3.79 c_mcangle_it 2.66 c_scbond_it 2.34 c_mcbond_it 1.52 c_angle_deg 1.3 c_improper_angle_d 0.94 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_scangle_it 3.79 c_mcangle_it 2.66 c_scbond_it 2.34 c_mcbond_it 1.52 c_angle_deg 1.3 c_improper_angle_d 0.94 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 3782 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 31
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling AMoRE phasing CNS refinement HKL-2000 data reduction