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Crystal structure of the P.falciparum cytosolic leucyl-tRNA synthetase editing domain (space group P21)
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 6.8 0.2 M SODIUM NITRATE (PH 6.8), 20% (W/V) PEG 3350, AND 12% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 1.8 33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.6 α = 90 b = 53.49 β = 97.31 c = 122.79 γ = 90
Symmetry Space Group P 1 21 1
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 2013-07-17 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 1.5 15 99 0.04 12 3.8 110127 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 1.5 1.6 99 0.8 1.5 3.4
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 1.5 50.01 94734 4943 99.33 0.18543 0.18282 0.1912 0.23408 0.2362 RANDOM 30.859
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] -3.49 1.07 -2.58 5.61
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 46.972 r_dihedral_angle_2_deg 35.914 r_sphericity_bonded 21.242 r_dihedral_angle_3_deg 12.941 r_dihedral_angle_4_deg 10.349 r_dihedral_angle_1_deg 5.981 r_mcangle_it 4.491 r_scbond_it 4.264 r_mcbond_it 3.743 r_mcbond_other 3.739
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 46.972 r_dihedral_angle_2_deg 35.914 r_sphericity_bonded 21.242 r_dihedral_angle_3_deg 12.941 r_dihedral_angle_4_deg 10.349 r_dihedral_angle_1_deg 5.981 r_mcangle_it 4.491 r_scbond_it 4.264 r_mcbond_it 3.743 r_mcbond_other 3.739 r_rigid_bond_restr 2.798 r_angle_refined_deg 1.607 r_angle_other_deg 1.082 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4925 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing