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Crystal structure of hte Cryptosporidium muris cytosolic leucyl-tRNA synthetase editing domain complex with a post-transfer editing analogue of norvaline (Nv2AA)
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 6.9 0.1 M KNO3 PH 6.9, 22% (W/V) PEG 3350. 20 % ETHYLENE GLYCOL AS CRYOPROTECTANT.
Crystal Properties Matthews coefficient Solvent content 3.4 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.73 α = 90 b = 107.73 β = 90 c = 309.51 γ = 90
Symmetry Space Group P 41 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 PIXEL DECTRIS PILATUS 6M 2014-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.3 15 99 0.1 16 8.1 81817 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 2.3 2.36 98 1.2 1.9 7.9
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 2.3 101.76 77686 4014 99.74 0.20261 0.20087 0.207 0.23607 0.2361 RANDOM 46.977
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] 0.91 0.91 1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.972 r_dihedral_angle_3_deg 14.495 r_dihedral_angle_4_deg 12.164 r_long_range_B_refined 6.744 r_long_range_B_other 6.744 r_dihedral_angle_1_deg 6.241 r_scangle_other 4.633 r_mcangle_it 3.891 r_mcangle_other 3.891 r_scbond_it 2.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.972 r_dihedral_angle_3_deg 14.495 r_dihedral_angle_4_deg 12.164 r_long_range_B_refined 6.744 r_long_range_B_other 6.744 r_dihedral_angle_1_deg 6.241 r_scangle_other 4.633 r_mcangle_it 3.891 r_mcangle_other 3.891 r_scbond_it 2.783 r_scbond_other 2.783 r_mcbond_it 2.351 r_mcbond_other 2.351 r_angle_refined_deg 1.382 r_angle_other_deg 0.893 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 8891 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing