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BRD4 in complex with FragLite33
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LRQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution
Crystal Properties Matthews coefficient Solvent content 2.09 41.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.746 α = 90 b = 43.221 β = 90 c = 78.538 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 2019-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.911628 Diamond I04-1
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 1.28 39.27 100 0.12 0.13 0.049 0.999 9.4 13.2 33928
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 1.28 1.3 7.399 8.011 3.048 0.372 13.1
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 5LRQ 1.28 39.27 33863 1648 99.959 0.217 0.2148 0.2155 0.2521 0.2548 22.343
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] 0.847 -1.73 0.883
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.001 r_dihedral_angle_4_deg 29.743 r_dihedral_angle_3_deg 13.23 r_dihedral_angle_1_deg 6.146 r_lrange_it 5.388 r_scangle_it 3.812 r_scbond_it 2.871 r_mcangle_it 2.44 r_angle_refined_deg 1.774 r_mcbond_it 1.717
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.001 r_dihedral_angle_4_deg 29.743 r_dihedral_angle_3_deg 13.23 r_dihedral_angle_1_deg 6.146 r_lrange_it 5.388 r_scangle_it 3.812 r_scbond_it 2.871 r_mcangle_it 2.44 r_angle_refined_deg 1.774 r_mcbond_it 1.717 r_nbtor_refined 0.328 r_nbd_refined 0.223 r_symmetry_nbd_refined 0.209 r_symmetry_xyhbond_nbd_refined 0.206 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.118 r_gen_planes_refined 0.011 r_bond_refined_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1076 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing