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Crystal Structure of Leishmania major Prolyl-tRNA Synthetase (LmPRS)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TWA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M Magnesium acetate and 20%(w/v) PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.33 47.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.294 α = 90 b = 98.861 β = 90 c = 146.327 γ = 90
Symmetry Space Group C 2 2 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 MARMOSAIC 225 mm CCD 2015-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.289 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.9 50 100 0.05 0.055 0.021 13.9 6.2 43411
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 100 0.414 0.45 0.176 0.934 6.2
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 4TWA 1.9 40.99 41101 2203 99.82 0.18237 0.17891 0.1846 0.2006 0.2132 RANDOM 23.183
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] -0.07 0.41 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.884 r_dihedral_angle_4_deg 17.081 r_dihedral_angle_3_deg 13.53 r_dihedral_angle_1_deg 6.553 r_angle_refined_deg 1.824 r_angle_other_deg 0.907 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.884 r_dihedral_angle_4_deg 17.081 r_dihedral_angle_3_deg 13.53 r_dihedral_angle_1_deg 6.553 r_angle_refined_deg 1.824 r_angle_other_deg 0.907 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3530 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 16
Software Software Software Name Purpose HKL-2000 data scaling SHELX phasing REFMAC refinement PDB_EXTRACT data extraction MxCuBE data reduction HKL data scaling SHELXD phasing