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Crystal structure of FKBP12 complexed with Small Molecule Anchor for Protein-201
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 8 277 0.1 M Tris-HCl (pH8.0), 3.0 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.02 39.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.577 α = 90 b = 48.039 β = 90 c = 65.306 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 PILATUS 6M 2025-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.000 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.26 38.7 99.6 0.161 8.4 17.5 27488
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.26 1.28 0.643
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2PPN 1.26 38.7 26041 1324 99.33 0.14889 0.14698 0.1596 0.18808 0.1966 RANDOM 11.591
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] -0.87 -0.56 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.373 r_dihedral_angle_4_deg 18.071 r_dihedral_angle_3_deg 13.857 r_dihedral_angle_1_deg 7.745 r_long_range_B_refined 3.857 r_long_range_B_other 3.451 r_rigid_bond_restr 2.769 r_scangle_other 2.715 r_scbond_it 2.099 r_scbond_other 2.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.373 r_dihedral_angle_4_deg 18.071 r_dihedral_angle_3_deg 13.857 r_dihedral_angle_1_deg 7.745 r_long_range_B_refined 3.857 r_long_range_B_other 3.451 r_rigid_bond_restr 2.769 r_scangle_other 2.715 r_scbond_it 2.099 r_scbond_other 2.097 r_angle_refined_deg 1.913 r_mcangle_other 1.912 r_mcangle_it 1.909 r_angle_other_deg 1.427 r_mcbond_it 1.341 r_mcbond_other 1.318 r_chiral_restr 0.224 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 832 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing