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First Bromodomain from Leishmania donovani LdBPK.091320 complexed with BI-2536
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TCK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 The protein was crystallized at 293 K with 2M NaFormate, 0.1M BTP 7.0 and 1.0 M Cesium chloride with BI2536 using the sitting drop method.
Crystal Properties Matthews coefficient Solvent content 2.8 61.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.332 α = 90 b = 85.25 β = 94.46 c = 57.277 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS3 S 6M 2016-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97880 APS 19-ID
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 2.2 50 99 0.132 0.148 0.065 4.8 4.5 24639 33.15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 97.2 0.585 0.818 4.3
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 5TCK 2.2 44.05 24471 1246 99 0.184 0.182 0.1838 0.218 0.2232 RANDOM 35.23
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] -4.8884 4.5978 9.5417 -4.6534
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.47 t_omega_torsion 3.72 t_angle_deg 0.67 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.47 t_omega_torsion 3.72 t_angle_deg 0.67 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle 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 2652 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 126
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing BUSTER-TNT refinement PDB_EXTRACT data extraction HKL-2000 data reduction