☰ Navigation Tabs
Tryptophan--tRNA ligase from Haemophilus influenzae.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N9I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 289 0.1 M potassium thiocyanate, 30% PEG MME 2000, 10 mM tryptophane
Crystal Properties Matthews coefficient Solvent content 2.21 44.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.294 α = 90 b = 48.677 β = 101.13 c = 99.322 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 210r 2017-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9792 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.05 50 99.9 0.122 0.141 0.071 8.9 3.8 42196
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 99.3 0.642 0.76 0.401 0.875 3.4
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 3N9I 2.05 35.5 40090 2084 98.01 0.1897 0.1872 0.1939 0.238 0.2454 RANDOM 37.432
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] -1.21 0.28 0.23 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.854 r_dihedral_angle_4_deg 20.257 r_dihedral_angle_3_deg 16.164 r_dihedral_angle_1_deg 5.794 r_angle_refined_deg 1.558 r_angle_other_deg 0.984 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.854 r_dihedral_angle_4_deg 20.257 r_dihedral_angle_3_deg 16.164 r_dihedral_angle_1_deg 5.794 r_angle_refined_deg 1.558 r_angle_other_deg 0.984 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5225 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 30
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 phasing