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Domain Swapped Bromodomain from Leishmania donovani
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 The protein (concentrated to 15mg/mL in 20mM HEPES pH 7.5 and 150 mM NaCl) was crystallized at 293 K in 30% PEG2000 MME, 0.15M KBr with bromosporine using the sitting drop method.
Crystal Properties Matthews coefficient Solvent content 2.32 46.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.176 α = 90 b = 77.176 β = 90 c = 169.496 γ = 120
Symmetry Space Group P 64 2 2
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 315 2015-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97921 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 2.6 50 98.9 0.099 0.102 0.025 10.1 17.7 9764
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 98.5 0.698 0.718 0.165 0.984 18.7 454
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 5C8G 2.6 50 9220 515 99.21 0.23 0.2275 0.2274 0.2772 0.2748 RANDOM 69.331
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] 2.15 1.08 2.15 -6.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.776 r_dihedral_angle_3_deg 12.92 r_dihedral_angle_4_deg 10.654 r_dihedral_angle_1_deg 5.069 r_mcangle_it 1.73 r_angle_refined_deg 1.136 r_angle_other_deg 1.06 r_mcbond_it 1.029 r_mcbond_other 1.028 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.776 r_dihedral_angle_3_deg 12.92 r_dihedral_angle_4_deg 10.654 r_dihedral_angle_1_deg 5.069 r_mcangle_it 1.73 r_angle_refined_deg 1.136 r_angle_other_deg 1.06 r_mcbond_it 1.029 r_mcbond_other 1.028 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1935 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 58
Software Software Software Name Purpose HKL-3000 data collection HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction