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Crystal structure of E.coli Histidyl-tRNA synthetase complexed with a histidyl-adenylate analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ADY PDB ENTRY 1ADY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1M HEPES, 0.5M NaCl, 14% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.26 62.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.113 α = 90 b = 108.345 β = 98.21 c = 193.645 γ = 90
Symmetry Space Group P 1 21 1
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 2006-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 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 2.7 50 95.4 0.085 6.4 64552 71
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 2.75 85.1 0.398 5.6
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 PDB ENTRY 1ADY 2.7 48.8 64526 6521 95.3 0.227 0.227 0.2242 0.285 0.2826 RANDOM 57.8
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] -10.48 -17.05 12.07 -1.59
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.7 c_scangle_it 10.27 c_scbond_it 8.19 c_mcangle_it 7.78 c_mcbond_it 5.61 c_angle_deg 1.6 c_improper_angle_d 1.57 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.7 c_scangle_it 10.27 c_scbond_it 8.19 c_mcangle_it 7.78 c_mcbond_it 5.61 c_angle_deg 1.6 c_improper_angle_d 1.57 c_bond_d 0.01 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 11718 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 132
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing