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Bromodomain from Trypanosoma brucei Tb427.10.8150
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O33
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 The 12 mg/ml (0.95 mM) protein in the base buffer (100 mM NaCl, 0.5 mM TCEP, 20 mM HEPES pH7,5) was crystallized at 20 ??C in 30% PEGM5K, 0.2 M NH4SO4, 0.1 M MES pH 6.5, in vapor diffusion sitting drop method. Final concentration of 3% DMSO and 1 mM SGC-CBP30 (IUPAC name: 8-(3-chloro-4-methoxy-phenethyl)-4-(3,5-dimethyl-isoxazol-4-yl)-9-(2-(morpholin-4-yl)-propyl)-7,9-diaza-bicyclo[4.3.0]nona-1(6),2,4,7-tetraene) was added to the concentrated protein immediately prior to setting up the crystallization plate.
Crystal Properties Matthews coefficient Solvent content 2.06 40.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.374 α = 90 b = 52.756 β = 117.27 c = 47.027 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 MARMOSAIC 300 mm CCD 2016-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97901 APS 22-ID
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 1.44 50 99.2 0.082 9.1 6.7 35635 15.47
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 1.44 1.46 96.5 0.358 4.5
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 3O33 1.44 41.8 35549 1865 99.2 0.162 0.161 0.1656 0.176 0.1801 RANDOM 17.65
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] 0.2775 -1.3632 -1.5866 1.3092
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.85 t_omega_torsion 3.62 t_angle_deg 0.74 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.85 t_omega_torsion 3.62 t_angle_deg 0.74 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1691 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 15
Software Software Software Name Purpose BUSTER refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction BALBES phasing