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FKBP12 in complex with binfunctional ligand b3c and the first bromodomain of BRD4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PPN experimental model PDB 7C2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25% PEG3350, 0.2M ammonium thiocyanate, 0.1 M Tris-HCl pH 8.8
Crystal Properties Matthews coefficient Solvent content 2.5 50.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.817 α = 90 b = 90.513 β = 90 c = 103.116 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 PILATUS3 S 6M 2024-11-07 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 3 48.72 99.9 0.306 0.332 0.127 0.989 8.9 12.5 11367
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) 3 3.18 100 0.66 0.713 0.269 0.936 4.3 13.2
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 THROUGHOUT 3 48.72 11326 596 99.789 0.263 0.26 0.2553 0.312 0.3077 26.841
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] -4.63 -0.726 5.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.593 r_dihedral_angle_3_deg 18.365 r_dihedral_angle_6_deg 14.699 r_dihedral_angle_1_deg 6.224 r_dihedral_angle_other_2_deg 3.396 r_angle_refined_deg 2.67 r_lrange_it 0.901 r_lrange_other 0.901 r_angle_other_deg 0.848 r_mcangle_it 0.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.593 r_dihedral_angle_3_deg 18.365 r_dihedral_angle_6_deg 14.699 r_dihedral_angle_1_deg 6.224 r_dihedral_angle_other_2_deg 3.396 r_angle_refined_deg 2.67 r_lrange_it 0.901 r_lrange_other 0.901 r_angle_other_deg 0.848 r_mcangle_it 0.826 r_mcangle_other 0.826 r_scangle_it 0.501 r_scangle_other 0.501 r_mcbond_it 0.478 r_mcbond_other 0.478 r_nbd_other 0.235 r_symmetry_nbd_other 0.232 r_nbd_refined 0.228 r_symmetry_nbd_refined 0.21 r_nbtor_refined 0.203 r_scbond_it 0.2 r_scbond_other 0.2 r_ncsr_local_group_2 0.188 r_symmetry_xyhbond_nbd_refined 0.172 r_xyhbond_nbd_refined 0.169 r_ncsr_local_group_1 0.163 r_chiral_restr 0.128 r_symmetry_nbtor_other 0.102 r_symmetry_xyhbond_nbd_other 0.072 r_bond_refined_d 0.019 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 3265 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement autoXDS data reduction Aimless data scaling PHASER phasing