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Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MW0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 1.8-2.1 M AMMONIUM SULFATE, 0.2 M
SODIUM CHLORIDE, 0.1 M SODIUM CACODYLATE, PH 6.2-6.8, VAPOR
DIFFUSION, SITTING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 3.96 68.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.96 α = 90 b = 106.32 β = 90 c = 207.59 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 PIXEL PSI PILATUS 6M 2015-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.98 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 103.79 99.7 5.5 5.9 60480
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.67
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 4MW0 2.6 103.79 57423 2965 99.55 0.21423 0.21284 0.2146 0.24122 0.2388 RANDOM 60.214
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] 5.67 -3.01 -2.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.39 r_dihedral_angle_4_deg 15.742 r_dihedral_angle_3_deg 13.26 r_long_range_B_refined 8.584 r_long_range_B_other 8.584 r_scangle_other 5.963 r_dihedral_angle_1_deg 5.684 r_mcangle_it 5.375 r_mcangle_other 5.375 r_angle_other_deg 3.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.39 r_dihedral_angle_4_deg 15.742 r_dihedral_angle_3_deg 13.26 r_long_range_B_refined 8.584 r_long_range_B_other 8.584 r_scangle_other 5.963 r_dihedral_angle_1_deg 5.684 r_mcangle_it 5.375 r_mcangle_other 5.375 r_angle_other_deg 3.686 r_scbond_it 3.667 r_scbond_other 3.665 r_mcbond_it 3.349 r_mcbond_other 3.348 r_angle_refined_deg 1.342 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8089 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement Aimless data scaling HKL-2000 data reduction PHASER phasing HKL-2000 data scaling