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FKBP12 in complex with bifunctional ligand a1d and the second bromodomain of BRD4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PPN experimental model PDB 7KO0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 18% PEG3350, 0.2M ammonium thiocyanate, 0.1M MES pH 6.5, 5 mM TEW
Crystal Properties Matthews coefficient Solvent content 3.19 61.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.422 α = 90 b = 80.422 β = 90 c = 212.044 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS3 X 6M 2025-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918400 BESSY 14.1
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 2.1 44.31 100 0.191 0.2 0.059 0.998 12.2 19 41683
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) 2.1 2.16 99.9 1.151 1.239 0.45 0.896 1.4 13.9
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 THROUGHOUT 2.1 44.3 39726 1943 95.472 0.247 0.2454 0.2352 0.2753 0.2616 24.487
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] 1.509 1.509 -3.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.354 r_dihedral_angle_6_deg 14.005 r_dihedral_angle_3_deg 13.608 r_dihedral_angle_1_deg 6.057 r_angle_refined_deg 3.828 r_lrange_it 3.356 r_lrange_other 3.337 r_scangle_it 2.069 r_scangle_other 2.069 r_mcangle_it 1.769
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.354 r_dihedral_angle_6_deg 14.005 r_dihedral_angle_3_deg 13.608 r_dihedral_angle_1_deg 6.057 r_angle_refined_deg 3.828 r_lrange_it 3.356 r_lrange_other 3.337 r_scangle_it 2.069 r_scangle_other 2.069 r_mcangle_it 1.769 r_mcangle_other 1.769 r_scbond_other 1.542 r_scbond_it 1.539 r_mcbond_it 1.016 r_mcbond_other 1.015 r_angle_other_deg 0.378 r_symmetry_xyhbond_nbd_refined 0.26 r_nbd_refined 0.201 r_symmetry_nbd_other 0.184 r_symmetry_nbd_refined 0.182 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.147 r_nbd_other 0.141 r_symmetry_nbtor_other 0.083 r_ncsr_local_group_2 0.083 r_ncsr_local_group_1 0.064 r_chiral_restr 0.058 r_bond_refined_d 0.018 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3359 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 207
Software Software Software Name Purpose REFMAC refinement autoXDS data reduction Aimless data scaling PHASER phasing