☰ Navigation Tabs
Crystal structure of a histidyl-tRNA synthetase HisRS from Burkholderia thailandensis bound to histidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HTT PDB entry 1HTT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 ButhA.00063.a.A1 PS01164 at 31 mg/mL with 5 mM L-histidine against Wizard III A3 focus screen, 350 mM magnesium formate, 12% PEG 3350 with 20% glycerol as cryo-protectant, crystal tracking ID 230808g3, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.81 56.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.16 α = 90 b = 116.36 β = 90 c = 142.99 γ = 90
Symmetry Space Group P 21 21 21
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 2012-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976484 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 2.65 50 99.5 0.065 24.34 7.8 34582 34582 -3 56.022
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 2.65 2.72 99.9 0.524 4.22
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 1HTT 2.65 19.61 34582 1742 99.46 0.2078 0.206 0.2067 0.2404 0.2409 RANDOM 51.8046
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] -3.91 5.78 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.258 r_dihedral_angle_4_deg 25.247 r_dihedral_angle_3_deg 15.453 r_dihedral_angle_1_deg 6.374 r_angle_refined_deg 1.464 r_angle_other_deg 1.13 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.258 r_dihedral_angle_4_deg 25.247 r_dihedral_angle_3_deg 15.453 r_dihedral_angle_1_deg 6.374 r_angle_refined_deg 1.464 r_angle_other_deg 1.13 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6041 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 22
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction