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Crystal structure of the Cryptosporidium muris cytosolic leucyl-tRNA synthetase editing domain complex with a post-transfer editing analogue of isoeucine (Ile2AA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WFG PDB ENTRY 2WFG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 1.4 M SODIUM/POTASSIUM PHOSPHATE PH 5.5. 20% GLYCEROL WAS USED AS CRYOPROTECTANT.
Crystal Properties Matthews coefficient Solvent content 2.6 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.957 α = 90 b = 64.957 β = 90 c = 167.292 γ = 90
Symmetry Space Group P 43 21 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 CCD ADSC QUANTUM 315r 2015-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U SSRF BL17U
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 1.77 50 99 0.15 31.2 14.6 25316 2
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 1.77 1.813 95.3 0.245 18.6
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 2WFG 1.77 35.44 29524 1573 86.37 0.1978 0.196 0.1961 0.23225 0.2256 RANDOM 24.742
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] 0.27 0.27 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.737 r_dihedral_angle_3_deg 14.47 r_dihedral_angle_4_deg 14.157 r_long_range_B_refined 6.628 r_dihedral_angle_1_deg 6.458 r_long_range_B_other 6.404 r_scangle_other 4.153 r_mcangle_it 2.756 r_mcangle_other 2.755 r_scbond_it 2.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.737 r_dihedral_angle_3_deg 14.47 r_dihedral_angle_4_deg 14.157 r_long_range_B_refined 6.628 r_dihedral_angle_1_deg 6.458 r_long_range_B_other 6.404 r_scangle_other 4.153 r_mcangle_it 2.756 r_mcangle_other 2.755 r_scbond_it 2.652 r_scbond_other 2.651 r_mcbond_it 1.81 r_mcbond_other 1.809 r_angle_refined_deg 1.677 r_angle_other_deg 0.971 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2189 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALA data scaling PHASER phasing