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Trypanosoma brucei methionyl-tRNA synthetase in complex with compound Chem 89
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EG1 PDB ENTRY 4EG1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 2.0 to 2.3M ammonium sulfate, 0.2M sodium chloride and 0.1M sodium cacodylate pH 6.0 to 6.6, vapor diffusion, sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.91 68.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.861 α = 90 b = 105.727 β = 90 c = 206.649 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 CCD MARMOSAIC 325 mm CCD 2011-07-17 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979 SSRL BL9-2
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 2.596 50 99.9 0.153 5.1 5 60150 -3
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 2.596 2.64 99.6 0.756 5
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 PDB ENTRY 4EG1 2.596 30 56834 3022 99.3 0.17915 0.17681 0.1834 0.22369 0.2272 RANDOM 37.592
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] 3.64 -1.86 -1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.788 r_dihedral_angle_3_deg 14.281 r_dihedral_angle_4_deg 14.236 r_dihedral_angle_1_deg 5.507 r_angle_refined_deg 1.177 r_angle_other_deg 0.832 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.788 r_dihedral_angle_3_deg 14.281 r_dihedral_angle_4_deg 14.236 r_dihedral_angle_1_deg 5.507 r_angle_refined_deg 1.177 r_angle_other_deg 0.832 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 8510 Nucleic Acid Atoms Solvent Atoms 461 Heterogen Atoms 161
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction