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Crystal Structure of L-3-(2-napthyl)alanine-tRNA synthetase in complex with L-3-(2-napthyl)alanine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 20% PEG-300, 5% PEG-8000,10% glycerol 0.1M Tris, pH 8.5, vapor diffusion,sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.7 54.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.995 α = 90 b = 102.995 β = 90 c = 71.441 γ = 90
Symmetry Space Group P 43 21 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 ADSC 2004-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.0 ALS 5.0.3
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 1.9 72.74 93.7 0.053 2.9 28143 33956
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 1.9 2.03 93.2 78.1 1.8
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 1.9 72.74 28143 28143 1507 96.09 0.222 0.222 0.22 0.2247 0.275 0.2847 RANDOM 50.724
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] 1.35 1.35 -2.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.888 r_dihedral_angle_3_deg 18.396 r_dihedral_angle_4_deg 15.731 r_scangle_it 6.357 r_dihedral_angle_1_deg 6.112 r_scbond_it 5.243 r_mcangle_it 2.483 r_mcbond_it 1.724 r_angle_refined_deg 1.574 r_angle_other_deg 1.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.888 r_dihedral_angle_3_deg 18.396 r_dihedral_angle_4_deg 15.731 r_scangle_it 6.357 r_dihedral_angle_1_deg 6.112 r_scbond_it 5.243 r_mcangle_it 2.483 r_mcbond_it 1.724 r_angle_refined_deg 1.574 r_angle_other_deg 1.099 r_symmetry_hbond_refined 0.448 r_nbd_refined 0.217 r_mcbond_other 0.216 r_symmetry_vdw_other 0.194 r_xyhbond_nbd_refined 0.192 r_nbd_other 0.184 r_nbtor_refined 0.183 r_xyhbond_nbd_other 0.157 r_chiral_restr 0.116 r_symmetry_vdw_refined 0.1 r_nbtor_other 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2461 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction