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BRD4-BD1 in complex with cyclic peptide 4.1C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LYI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M HEPES pH 7.5, 42% v/v Polyethylene glycol 200
Crystal Properties Matthews coefficient Solvent content 2.39 48.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.121 α = 90 b = 70.121 β = 90 c = 90.16 γ = 120
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 EIGER X 16M 2018-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.73 19.751 94.6 0.147 0.999 7.5 7.4 45685
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.832 47.3 1.367 0.242 1.3 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.73 19.751 45684 2051 88.162 0.177 0.1757 0.1897 0.2129 0.2284 29.237
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] -0.271 -0.271 0.542
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.036 r_dihedral_angle_3_deg 12.828 r_dihedral_angle_2_deg 9.554 r_lrange_other 6.41 r_lrange_it 6.409 r_dihedral_angle_1_deg 5.65 r_scangle_it 5.572 r_scangle_other 5.571 r_mcangle_it 4.659 r_mcangle_other 4.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.036 r_dihedral_angle_3_deg 12.828 r_dihedral_angle_2_deg 9.554 r_lrange_other 6.41 r_lrange_it 6.409 r_dihedral_angle_1_deg 5.65 r_scangle_it 5.572 r_scangle_other 5.571 r_mcangle_it 4.659 r_mcangle_other 4.658 r_scbond_it 4.386 r_scbond_other 4.385 r_mcbond_it 3.854 r_mcbond_other 3.843 r_angle_refined_deg 1.862 r_angle_other_deg 0.657 r_symmetry_nbd_refined 0.356 r_nbd_other 0.226 r_nbd_refined 0.212 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_other 0.182 r_symmetry_xyhbond_nbd_refined 0.157 r_xyhbond_nbd_refined 0.147 r_ncsr_local_group_4 0.104 r_chiral_restr 0.101 r_ncsr_local_group_6 0.098 r_ncsr_local_group_1 0.089 r_symmetry_nbtor_other 0.087 r_ncsr_local_group_5 0.083 r_ncsr_local_group_2 0.078 r_ncsr_local_group_3 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3299 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing