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Crystal structure of the second bromodomain of BRD5 from Leishmania donovani
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TCK 5TCK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.1 M HEPES pH 7.5 and 1.4 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.1 41.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.37 α = 90 b = 75.356 β = 90 c = 105.798 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 PIXEL DECTRIS PILATUS 6M-F 2018-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.6 31.845 98.3 0.047 0.054 0.025 0.999 19.4 8.1 35399
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 1.6 1.63 0.568 0.646 0.304 0.928 8.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5TCK 1.6 31.845 35358 1701 97.893 0.164 0.1615 0.2095 0.2147 0.2509 17.081
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] 2.076 -2.183 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.436 r_dihedral_angle_3_deg 15.855 r_dihedral_angle_2_deg 11.057 r_dihedral_angle_1_deg 4.694 r_scangle_it 4.371 r_scangle_other 4.37 r_rigid_bond_restr 4.154 r_lrange_it 4.153 r_lrange_other 4.13 r_scbond_it 3.951
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.436 r_dihedral_angle_3_deg 15.855 r_dihedral_angle_2_deg 11.057 r_dihedral_angle_1_deg 4.694 r_scangle_it 4.371 r_scangle_other 4.37 r_rigid_bond_restr 4.154 r_lrange_it 4.153 r_lrange_other 4.13 r_scbond_it 3.951 r_scbond_other 3.945 r_mcangle_it 3.278 r_mcangle_other 3.277 r_mcbond_it 2.77 r_mcbond_other 2.768 r_angle_refined_deg 1.402 r_symmetry_nbd_refined 0.78 r_angle_other_deg 0.493 r_nbd_other 0.386 r_nbd_refined 0.229 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.172 r_symmetry_xyhbond_nbd_other 0.122 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2212 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction pointless data scaling Coot model building