8PDF

FKBP12 in complex with PROTAC 6a2

X-RAY DIFFRACTION

---

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	1.36 Na/K tartrate, 0.2M ammonium citrate, 0.1M MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.993	α = 90
b = 36.506	β = 102.186
c = 44.217	γ = 90

Symmetry
Space Group	C 1 2 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	1.2	43.22	99.9	0.055	0.066	0.036	0.999	11.7	6.3		32330

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	1.2	1.22			1.318	1.599	0.892	0.625		6

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.2	31.791	32324	1615	99.91	0.153	0.1516	0.1756	17.843

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]
1.127		0.489	-0.995		-0.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.602
r_dihedral_angle_3_deg	13.366
r_dihedral_angle_1_deg	7.191
r_dihedral_angle_2_deg	6.487
r_rigid_bond_restr	4.118
r_lrange_it	3.892
r_lrange_other	3.127
r_scangle_it	2.314
r_scangle_other	2.314
r_angle_refined_deg	1.969
r_mcangle_it	1.815
r_mcangle_other	1.813
r_scbond_it	1.776
r_scbond_other	1.774
r_chiral_restr_other	1.576
r_mcbond_it	1.392
r_mcbond_other	1.392
r_angle_other_deg	1.159
r_chiral_restr	0.307
r_symmetry_xyhbond_nbd_refined	0.25
r_nbd_refined	0.218
r_symmetry_nbd_other	0.213
r_symmetry_nbd_refined	0.188
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.168
r_nbd_other	0.167
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.017
r_gen_planes_refined	0.011
r_bond_other_d	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	820
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	70

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing