8BA6 | pdb_00008ba6

Structure of the FK1 domain of the FKBP51 G64S variant in complex with (2R,5S,12R)-12-cyclohexyl-2-[2-(3,4-dimethoxyphenyl)ethyl]-15,15,16-trimethyl-3,19-dioxa-10,13,16-triazatricyclo[18.3.1.0^5,^10]tetracosa-1(24),20,22-triene-4,11,14,17-tetrone

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7AWF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	30% PEG3350 0.2M ammonium acetate 0.1 M HEPES-NaOH pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.575	α = 90
b = 50.42	β = 90
c = 59.073	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 PILATUS3 S 6M		2021-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	1.1	38.35	95.2	0.052	0.061	0.032	1	16.5	6.6		50803

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	1.1	1.12			0.781	0.92	0.483	0.745		6.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7AWF	1.1	29.554	50756	2537	94.784	0.141	0.1397	0.14	0.1604	0.16	12.06

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]
-2.398			1.71		0.688

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.351
r_rigid_bond_restr	14.333
r_dihedral_angle_3_deg	11.984
r_dihedral_angle_1_deg	7.955
r_dihedral_angle_2_deg	6.353
r_lrange_it	5.503
r_lrange_other	4.561
r_scangle_it	4.248
r_scangle_other	4.245
r_scbond_it	4.221
r_scbond_other	4.217
r_mcangle_it	3.563
r_mcangle_other	3.561
r_mcbond_it	3.276
r_mcbond_other	3.276
r_angle_refined_deg	1.77
r_chiral_restr_other	1.181
r_angle_other_deg	1.013
r_nbd_refined	0.263
r_symmetry_nbd_refined	0.259
r_nbd_other	0.204
r_xyhbond_nbd_refined	0.201
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.168
r_chiral_restr	0.108
r_symmetry_nbtor_other	0.084
r_gen_planes_refined	0.014
r_bond_refined_d	0.013
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	975
Nucleic Acid Atoms
Solvent Atoms	221
Heterogen Atoms	49

Software

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