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Crystal structure of a tryptophanyl-tRNA synthetase from Encephalitozoon cuniculi bound to tryptophan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ULH PDB entry 1ULH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 EncuA.00600.a.A1 PS00344 at 23.5 mg/mL against Wizard III screen from Emerald BioSystems, 20% PEG 3350, 0.2 M potassium nitrate, crystal tracking ID 221699a8, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.04 39.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.11 α = 90 b = 79.16 β = 90 c = 177.01 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 2011-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-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 2.6 50 96.5 0.078 14.71 4.8 24185 23335 -3 48.833
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 2.6 2.67 89.5 0.517 2.23 3.4 1760
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1ULH 2.6 50 24185 23335 1191 96.48 0.2044 0.2021 0.2025 0.2472 0.2458 RANDOM 43.2257
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] -1.31 -0.12 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.461 r_dihedral_angle_3_deg 17.821 r_dihedral_angle_4_deg 15.044 r_dihedral_angle_1_deg 6.3 r_angle_refined_deg 1.392 r_chiral_restr 0.098 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5379 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 32
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction