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Human FKBP12 in complex with (1S,5S,6R)-10-((S)-3,5-dichloro-N-methylphenylsulfonimidoyl)-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, HANGING DROP 293 1.4M Na/K tartrate, 0.2 M ammonium citrate, 0.1M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.3 62.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.361 α = 90 b = 69.361 β = 90 c = 129.848 γ = 90
Symmetry Space Group P 41 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 S 2M 2021-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918400 BESSY 14.2
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 1.7 47.444 100 0.114 0.118 0.032 1 22.2 25.7 35735
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 1.7 1.73 1.776 1.842 0.488 0.732 27.2
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 1.7 47.444 35656 1703 99.978 0.18 0.178 0.1774 0.2144 0.2135 21.329
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] -0.107 -0.107 0.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.543 r_dihedral_angle_3_deg 14.511 r_dihedral_angle_2_deg 10.431 r_dihedral_angle_1_deg 7.295 r_lrange_it 5.91 r_lrange_other 5.78 r_scangle_it 4.589 r_scangle_other 4.587 r_scbond_other 3.288 r_scbond_it 3.286
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.543 r_dihedral_angle_3_deg 14.511 r_dihedral_angle_2_deg 10.431 r_dihedral_angle_1_deg 7.295 r_lrange_it 5.91 r_lrange_other 5.78 r_scangle_it 4.589 r_scangle_other 4.587 r_scbond_other 3.288 r_scbond_it 3.286 r_mcangle_it 2.992 r_mcangle_other 2.991 r_mcbond_other 2.119 r_mcbond_it 2.118 r_chiral_restr_other 1.979 r_angle_refined_deg 1.799 r_angle_other_deg 0.824 r_nbd_refined 0.222 r_symmetry_nbd_refined 0.214 r_symmetry_nbd_other 0.195 r_nbd_other 0.19 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.139 r_ncsr_local_group_1 0.137 r_symmetry_xyhbond_nbd_refined 0.132 r_symmetry_xyhbond_nbd_other 0.094 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1628 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing