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Co-crystal structure of the ternary complex of human FKBP12, QDPR and Compound 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7U8D experimental model PDB 1HDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.1 M TRIS-HCL PH 7, 0.2 M CALCIUM ACETATE
HYDRATE, 20 % (W/V) PEG 3000 (MCSG SCREEN 1, CONDITION C11); 1:1:1 FKBP12:QDPR:MOTHER LIQUOR PLUS EQUIMOLAR COMPOUND IN 200-NL DROP. COMPLEX CONCENTRATED TO 10 MG/ML
Crystal Properties Matthews coefficient Solvent content 3.11 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.937 α = 90 b = 61.416 β = 90 c = 69.971 γ = 90
Symmetry Space Group P 21 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 EIGER2 X CdTe 16M 2024-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97621 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.39 53.62 99.8 0.066 0.998 13.1 9.4 95389
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 1.39 1.394 0.312
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.39 30.4 1.34 95389 4800 99.25 0.1902 0.1889 0.1899 0.2142 0.2143
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.561 f_angle_d 1.871 f_chiral_restr 0.116 f_bond_d 0.025 f_plane_restr 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2590 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 74
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing