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BRD4 in complex with PepLite-Val
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 2.13 42.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.808 α = 90 b = 43.417 β = 90 c = 79.36 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 2019-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.953970 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 1.08 39.68 95.5 0.073 0.086 0.045 0.998 8 6.1 54177
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 1.08 1.1 1.413 1.821 1.136 0.327 3.1
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 1.08 39.68 54111 2655 95.182 0.207 0.2056 0.2057 0.2364 0.2365 17.505
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] 0.381 -0.298 -0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.326 r_dihedral_angle_4_deg 26.845 r_dihedral_angle_3_deg 12.55 r_lrange_it 6.935 r_dihedral_angle_1_deg 6.234 r_scangle_it 4.826 r_scbond_it 3.643 r_angle_refined_deg 2.078 r_mcangle_it 1.988 r_mcbond_it 1.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.326 r_dihedral_angle_4_deg 26.845 r_dihedral_angle_3_deg 12.55 r_lrange_it 6.935 r_dihedral_angle_1_deg 6.234 r_scangle_it 4.826 r_scbond_it 3.643 r_angle_refined_deg 2.078 r_mcangle_it 1.988 r_mcbond_it 1.335 r_nbtor_refined 0.324 r_nbd_refined 0.245 r_symmetry_nbd_refined 0.211 r_xyhbond_nbd_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.168 r_chiral_restr 0.115 r_bond_refined_d 0.014 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1076 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing