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Human FKBP12 in complex with (1S,5S,6R)-9-((3,5-dichlorophenyl)sulfonyl)-3-(pyridin-2-ylmethyl)-5-vinyl-3,9-diazabicyclo[4.2.1]nonan-2-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PPN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.2 M ammonium sulfate, 0.2 M cadmium sulfate
Crystal Properties Matthews coefficient Solvent content 2.56 51.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.582 α = 90 b = 70.582 β = 90 c = 84.263 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 PILATUS3 S 6M 2021-12-18 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 1.4 42.13 99.8 0.073 0.083 0.039 0.999 13.6 7.5 46787
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 1.4 1.42 1.518 1.862 1.052 0.313 3.6
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 1.4 35.316 46741 2257 99.772 0.189 0.1876 0.186 0.2128 0.2146 15.121
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] -0.011 -0.006 -0.011 0.036
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.583 r_dihedral_angle_3_deg 12.575 r_dihedral_angle_1_deg 7.707 r_dihedral_angle_2_deg 5.444 r_lrange_it 5.207 r_lrange_other 5.021 r_scangle_it 3.616 r_scangle_other 3.568 r_mcangle_it 2.673 r_mcangle_other 2.672
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.583 r_dihedral_angle_3_deg 12.575 r_dihedral_angle_1_deg 7.707 r_dihedral_angle_2_deg 5.444 r_lrange_it 5.207 r_lrange_other 5.021 r_scangle_it 3.616 r_scangle_other 3.568 r_mcangle_it 2.673 r_mcangle_other 2.672 r_scbond_it 2.573 r_scbond_other 2.539 r_chiral_restr_other 2.192 r_angle_refined_deg 1.743 r_mcbond_it 1.698 r_mcbond_other 1.698 r_angle_other_deg 0.887 r_symmetry_xyhbond_nbd_refined 0.316 r_nbd_refined 0.209 r_symmetry_nbd_other 0.202 r_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.182 r_symmetry_nbd_refined 0.178 r_nbd_other 0.178 r_symmetry_metal_ion_refined 0.16 r_chiral_restr 0.155 r_ncsr_local_group_1 0.122 r_metal_ion_refined 0.093 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1610 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing