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Human FKBP12 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophenyl)sulfinyl)-3-(pyridin-2-ylmethyl)-5-vinyl-3,10-diazabicyclo[4.3.1]decan-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 2.1 M ammonium sulfate, 0.2 M cadmium chloride, 0.1M HEPES-NaOH pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.75 55.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.592 α = 90 b = 40.081 β = 90 c = 91.212 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 2022-09-10 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 1.12 45.648 99.7 0.026 0.03 0.015 0.999 30.7 7 50936
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 1.12 1.14 0.096 0.111 0.056 0.996 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 THROUGHOUT 1.12 45.648 50866 2537 99.626 0.131 0.13 0.13 0.1455 0.1448 10.321
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] 1.555 -0.7 -0.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.161 r_dihedral_angle_3_deg 13.306 r_dihedral_angle_1_deg 7.059 r_rigid_bond_restr 5.011 r_dihedral_angle_2_deg 4.006 r_lrange_it 2.808 r_chiral_restr_other 2.231 r_lrange_other 2.107 r_angle_refined_deg 1.878 r_scangle_it 1.659
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.161 r_dihedral_angle_3_deg 13.306 r_dihedral_angle_1_deg 7.059 r_rigid_bond_restr 5.011 r_dihedral_angle_2_deg 4.006 r_lrange_it 2.808 r_chiral_restr_other 2.231 r_lrange_other 2.107 r_angle_refined_deg 1.878 r_scangle_it 1.659 r_scangle_other 1.645 r_scbond_it 1.337 r_scbond_other 1.329 r_mcangle_it 0.873 r_mcangle_other 0.872 r_angle_other_deg 0.864 r_mcbond_it 0.687 r_mcbond_other 0.687 r_symmetry_xyhbond_nbd_refined 0.335 r_xyhbond_nbd_refined 0.275 r_symmetry_nbd_refined 0.253 r_nbd_refined 0.235 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.179 r_nbd_other 0.176 r_chiral_restr 0.165 r_metal_ion_refined 0.154 r_symmetry_metal_ion_refined 0.099 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 814 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing