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Crystal structure of Pyrococcus horikoshii tryptophanyl-tRNA synthetase in complex with TrpAMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 293 0.1M sodium citrate, 1.6M (NH4)2SO4, 10mM MnCl2, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.45 72.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.198 α = 90 b = 170.198 β = 90 c = 170.198 γ = 90
Symmetry Space Group P 21 3
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 270 2008-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000 Photon Factory BL-17A
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 3 50 100 0.088 33.1 15.5 33131 99.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3 3.11 99.5 0.788 2.6 10.3 3255
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3 50 33089 1650 99.9 0.239 0.238 0.235 0.258 0.2377 RANDOM 79.725
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.252 r_dihedral_angle_3_deg 16.929 r_dihedral_angle_4_deg 14.44 r_dihedral_angle_1_deg 4.77 r_angle_refined_deg 0.985 r_scangle_it 0.772 r_scbond_it 0.55 r_mcangle_it 0.547 r_mcbond_it 0.35 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.252 r_dihedral_angle_3_deg 16.929 r_dihedral_angle_4_deg 14.44 r_dihedral_angle_1_deg 4.77 r_angle_refined_deg 0.985 r_scangle_it 0.772 r_scbond_it 0.55 r_mcangle_it 0.547 r_mcbond_it 0.35 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.228 r_nbd_refined 0.178 r_symmetry_hbond_refined 0.145 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6035 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing