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Human FKBP12 in complex with (1S,5S,6R)-10-((R)-(3,5-dichlorophenyl)sulfonimidoyl)-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 1.32M Na-K tartrate, 0.2 M ammonium citrate, 0.1M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.76 55.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.716 α = 90 b = 80.12 β = 91.072 c = 66.895 γ = 90
Symmetry Space Group P 1 21 1
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 1.697 48.755 99.7 0.071 0.084 0.045 0.999 13.2 6.7 56711
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 1.007 1.193 0.634 0.711 6.5
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 1.697 48.755 56687 2813 99.766 0.184 0.1828 0.1822 0.2047 0.2044 25.864
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] 1.764 -1.43 -0.597 -1.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.426 r_dihedral_angle_3_deg 13.558 r_dihedral_angle_2_deg 9.425 r_dihedral_angle_1_deg 7.251 r_lrange_it 5.78 r_lrange_other 5.729 r_scangle_it 3.931 r_scangle_other 3.93 r_mcangle_it 2.688 r_mcangle_other 2.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.426 r_dihedral_angle_3_deg 13.558 r_dihedral_angle_2_deg 9.425 r_dihedral_angle_1_deg 7.251 r_lrange_it 5.78 r_lrange_other 5.729 r_scangle_it 3.931 r_scangle_other 3.93 r_mcangle_it 2.688 r_mcangle_other 2.688 r_scbond_it 2.653 r_scbond_other 2.652 r_chiral_restr_other 2.143 r_mcbond_it 1.839 r_mcbond_other 1.839 r_angle_refined_deg 1.664 r_angle_other_deg 0.884 r_symmetry_nbd_refined 0.237 r_nbd_other 0.236 r_nbd_refined 0.226 r_symmetry_xyhbond_nbd_refined 0.21 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.143 r_ncsr_local_group_4 0.114 r_ncsr_local_group_1 0.107 r_ncsr_local_group_6 0.107 r_ncsr_local_group_3 0.106 r_ncsr_local_group_2 0.101 r_symmetry_nbtor_other 0.085 r_ncsr_local_group_5 0.082 r_symmetry_xyhbond_nbd_other 0.053 r_bond_refined_d 0.012 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 3237 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing