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Crystal structure of Trypanosoma brucei AdoMetDC/prozyme heterodimer in complex with pyrimidineamine inhibitor UTSAM568
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TVM PDB entry 5TVM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1 uL 4 mg/mL protein in crystallization buffer (50 mM Bis-Tris propane, pH 7.2, 50 mM sodium chloride, 4 mM TCEP, 2 mM putrescine, 0.5 mM N4-(3,5-dibromophenyl)-6-methylpyrimidine-2,4-diamine [UTSAM568], 1% DMSO) + 1 uL reservoir solution (17% PEG6000, 100 mM Bis-Tris propane, pH 7.0) + 0.5 uL unliganded protein microseeds obtained using Seed-Bead method in stabilization solution (100 mM Bis-Tris propane, pH 8.9, 50 mM HEPES, pH 7.2, 19% PEG6000, 50 mM sodium chloride, 4 mM TCEP, 2 mM putrescine)
Crystal Properties Matthews coefficient Solvent content 2.6 52.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.09 α = 90 b = 96.25 β = 102.426 c = 98.84 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 CCD ADSC QUANTUM 315r 2015-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.91905 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.98 50 99.8 0.194 0.074 10 6.8 30294 49.2238648407
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.05 99.1 0.712 1.87 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 5TVM 2.98 48.2623233532 1.33789805147 50644 2520 84.6026628356 0.202335356515 0.199589623624 0.2035 0.254857270037 0.2546 58.4151476361
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.4170911814 f_angle_d 0.558602768216 f_chiral_restr 0.0446252615216 f_plane_restr 0.00364942909324 f_bond_d 0.00314584829052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10193 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 117
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing