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Crystal structure of the P.falciparum cytosolic leucyl-tRNA synthetase editing domain (space group P1) containing deletions of insertions 1 and 3
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), 20% (W/V) PEG 10000, AND 8% ETHYLENEGLYCOL
Crystal Properties Matthews coefficient Solvent content 2 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.6 α = 88.4 b = 53.1 β = 73.7 c = 62.7 γ = 89.8
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 1.7 15 94 0.09 6 2.7 62051 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 1.7 1.75 88 0.9 0.8 2
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 1.7 60.16 59030 3020 93.75 0.20517 0.20262 0.2097 0.25506 0.2622 RANDOM 34.07
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] -1.11 0.43 -0.83 -0.11 -0.43 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.207 r_dihedral_angle_3_deg 14.519 r_dihedral_angle_4_deg 12.518 r_dihedral_angle_1_deg 6.252 r_mcangle_it 3.703 r_scbond_it 3.405 r_mcbond_it 2.573 r_mcbond_other 2.566 r_angle_refined_deg 1.607 r_angle_other_deg 0.985
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.207 r_dihedral_angle_3_deg 14.519 r_dihedral_angle_4_deg 12.518 r_dihedral_angle_1_deg 6.252 r_mcangle_it 3.703 r_scbond_it 3.405 r_mcbond_it 2.573 r_mcbond_other 2.566 r_angle_refined_deg 1.607 r_angle_other_deg 0.985 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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_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 5093 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing