☰ Navigation Tabs
Crystal structure of cysteinyl-tRNA synthetase (cysS) from Borrelia burgdorferi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LI5 pdb entry 1LI5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 protein at 25 mg/mL against PACT E9 25% PEG 3350, 0.2 M Na K Tartrate with 25% ethylene glycol as cryo-protectant, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.4 48.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.62 α = 90 b = 49.89 β = 93.18 c = 179.63 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 315r 2011-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 ALS 5.0.1
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 99.5 0.107 12.48 4.6 36778 36598 -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) 1 2.55 2.62 99 0.524 2.52
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 1LI5 2.55 50 34652 1835 99.21 0.2268 0.22433 0.2236 0.27398 0.2719 RANDOM 29.145
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] 0.18 0.11 1.18 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.247 r_dihedral_angle_4_deg 22.65 r_dihedral_angle_3_deg 16.832 r_dihedral_angle_1_deg 6.258 r_scangle_it 2.803 r_scbond_it 1.741 r_angle_refined_deg 1.538 r_mcangle_it 1.2 r_mcbond_it 0.628 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.247 r_dihedral_angle_4_deg 22.65 r_dihedral_angle_3_deg 16.832 r_dihedral_angle_1_deg 6.258 r_scangle_it 2.803 r_scbond_it 1.741 r_angle_refined_deg 1.538 r_mcangle_it 1.2 r_mcbond_it 0.628 r_chiral_restr 0.11 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6808 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 49
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction