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Crystal structure of the P.knowlesi cytosolic leucyl-tRNA synthetase editing domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other CRYPTOSPORIDIUM MURIS LEUCYL-TRNA SYNTHETASE EDITING DOMAIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.05 M SODIUM CACODYLATE (PH 6.5), 0.2 M POTASSIUM CHLORIDE, 0.1 M MAGNESIUM ACETATE, 10% (W/V) PEG 8000, AND 25% ETHYLENEGLYCOL
Crystal Properties Matthews coefficient Solvent content 2.4 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.03 α = 90 b = 96.82 β = 90 c = 168.91 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 2012-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.4 15 99 0.07 15 4.5 60544 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 2.4 2.49 95 0.8 2.2 4.5
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 CRYPTOSPORIDIUM MURIS LEUCYL-TRNA SYNTHETASE EDITING DOMAIN 2.4 84.46 57478 3066 99.7 0.22141 0.21816 0.22 0.2803 0.2796 RANDOM 59.294
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] 1.09 4.15 -5.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.616 r_dihedral_angle_4_deg 15.898 r_dihedral_angle_3_deg 15.303 r_dihedral_angle_1_deg 6.56 r_mcangle_it 4.944 r_scbond_it 3.165 r_mcbond_it 3.112 r_mcbond_other 3.108 r_angle_refined_deg 1.318 r_angle_other_deg 0.895
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.616 r_dihedral_angle_4_deg 15.898 r_dihedral_angle_3_deg 15.303 r_dihedral_angle_1_deg 6.56 r_mcangle_it 4.944 r_scbond_it 3.165 r_mcbond_it 3.112 r_mcbond_other 3.108 r_angle_refined_deg 1.318 r_angle_other_deg 0.895 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9831 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing