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BRD4 in complex with FragLite10
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 2.08 40.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.589 α = 90 b = 42.962 β = 90 c = 78.767 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 2019-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91188 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 1.04 39.38 100 0.082 0.089 0.034 0.999 11.3 12.3 62122
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 1.04 1.06 6.264 6.964 3.02 0.41 10.1
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 1.04 39.38 62033 3095 99.942 0.212 0.211 0.2112 0.2333 0.2335 18.865
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] 1.336 -1.173 -0.164
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 7.326 r_dihedral_angle_1_deg 6.168 r_scangle_it 4.944 r_dihedral_angle_2_deg 3.805 r_scbond_it 3.447 r_mcangle_it 2.352 r_angle_refined_deg 1.963 r_mcbond_it 1.725 r_symmetry_nbd_refined 0.375 r_nbtor_refined 0.333
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 7.326 r_dihedral_angle_1_deg 6.168 r_scangle_it 4.944 r_dihedral_angle_2_deg 3.805 r_scbond_it 3.447 r_mcangle_it 2.352 r_angle_refined_deg 1.963 r_mcbond_it 1.725 r_symmetry_nbd_refined 0.375 r_nbtor_refined 0.333 r_nbd_refined 0.263 r_symmetry_xyhbond_nbd_refined 0.248 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.11 r_gen_planes_refined 0.014 r_bond_refined_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1076 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing