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Crystal structure of the P.falciparum cytosolic leucyl-tRNA synthetase editing domain (space group P1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other PLASMODIUM KNOWLESI LEURS EDITING DOMAIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1 M HEPES (PH 7.5), 10% ISOPROPANOL, 20% (W/V) PEG 4000 AND 5% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 1.8 32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.7 α = 88.9 b = 53.4 β = 74.3 c = 63 γ = 89.7
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 2013-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.85 15 87 0.06 8.7 1.8 45297 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 1.9 2 84 0.52 1.6 1.9
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 PLASMODIUM KNOWLESI LEURS EDITING DOMAIN 1.85 60.64 43145 2151 86.89 0.19737 0.19461 0.202 0.25214 0.2573 RANDOM 36.235
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] -1.79 0.5 -0.36 1.49 -0.87 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.8 r_dihedral_angle_3_deg 14.366 r_dihedral_angle_4_deg 11.68 r_dihedral_angle_1_deg 6.104 r_mcangle_it 4.178 r_scbond_it 3.726 r_mcbond_it 2.816 r_mcbond_other 2.814 r_angle_refined_deg 1.58 r_angle_other_deg 1.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.8 r_dihedral_angle_3_deg 14.366 r_dihedral_angle_4_deg 11.68 r_dihedral_angle_1_deg 6.104 r_mcangle_it 4.178 r_scbond_it 3.726 r_mcbond_it 2.816 r_mcbond_other 2.814 r_angle_refined_deg 1.58 r_angle_other_deg 1.023 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 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_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 5099 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing