8CCF | pdb_00008ccf

The Fk1 domain of FKBP51 in complex with 2-(3-((R)-1-(((S)-1-((S)-2-(5-chlorothiophen-2-yl)pent-4-enoyl)piperidine-2-carbonyl)oxy)-3-(3,4-dimethoxyphenyl)propyl)phenoxy)acetic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4TW7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	20% PEG3350, 0.1 M HEPES pH 7.5, 0.2 M ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.295	α = 90
b = 48.302	β = 90
c = 57.238	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 6M		2022-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918400	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	2	48.3	99.8	0.044	0.052	0.026	0.999	21.7	7		9295

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	2	2.05			0.473	0.549	0.275	0.941		7.3

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	4TW7	2	36.486	9261	436	99.602	0.211	0.2089	0.21	0.2463	0.25	46.877

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]
7.421			-4.017		-3.404

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.969
r_dihedral_angle_3_deg	12.838
r_dihedral_angle_1_deg	8.52
r_lrange_it	6.89
r_lrange_other	6.887
r_mcangle_other	4.553
r_mcangle_it	4.548
r_scangle_it	4.347
r_scangle_other	4.344
r_mcbond_other	3.094
r_mcbond_it	3.09
r_scbond_it	2.909
r_scbond_other	2.906
r_dihedral_angle_2_deg	2.882
r_angle_refined_deg	1.656
r_chiral_restr_other	0.748
r_angle_other_deg	0.626
r_nbd_refined	0.224
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.18
r_nbd_other	0.176
r_xyhbond_nbd_refined	0.139
r_symmetry_xyhbond_nbd_refined	0.1
r_symmetry_nbd_refined	0.093
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.067
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	934
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms	45

Software

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