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lysyl-tRNA Synthetase (LYSU) hexagonal form, complexed with lysine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LYL PDB ENTRY 1LYL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.8 PROTEIN WAS CRYSTALLISED FROM 0.1M PIPES PH 6.8, 0.5 M LICL; 20% PEG 4K, 17% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 4.8 74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.1 α = 90 b = 143.1 β = 90 c = 176.1 γ = 120
Symmetry Space Group P 61 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 IMAGE PLATE MARRESEARCH MIRROR 1995-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.12 25 99.6 0.085 0.085 8.8 16.2 60434
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.16 99.6 0.26 0.26 3.7 15.4
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 1LYL 2.12 20 57124 2301 99.6 0.195 0.195 0.1883 0.233 0.2219 RANDOM
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 x_dihedral_angle_d 23.7 x_scangle_it 6.41 x_scbond_it 4.11 x_mcangle_it 3.36 x_mcbond_it 2.13 x_angle_deg 1.6 x_improper_angle_d 1.17 x_bond_d 0.007 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 23.7 x_scangle_it 6.41 x_scbond_it 4.11 x_mcangle_it 3.36 x_mcbond_it 2.13 x_angle_deg 1.6 x_improper_angle_d 1.17 x_bond_d 0.007 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3815 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 58
Software Software Software Name Purpose X-PLOR refinement MOSFLM data reduction CCP4 data scaling X-PLOR phasing