8CCC | pdb_00008ccc

The Fk1 domain of FKBP51 in complex with 2-(3-((R)-1-(((S)-1-((S)-2-(5-chlorothiophen-2-yl)propanoyl)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	22% PEG3350, 0.1 M HEPES pH 7.5, 0.2 M ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.651	α = 90
b = 50.882	β = 90
c = 58.103	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		2021-09-21	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	1.55	48.65	99.9	0.054	0.059	0.024	0.999	18.4	10.9		21573

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	1.55	1.58			1.218	1.353	0.581	0.809		10

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	1.55	38.308	21412	1064	99.364	0.217	0.2161	0.22	0.2389	0.24	32.336

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]
-1.935			5.595		-3.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.062
r_dihedral_angle_3_deg	13.475
r_dihedral_angle_1_deg	8.545
r_lrange_it	6.036
r_lrange_other	5.987
r_dihedral_angle_2_deg	4.202
r_scangle_it	3.492
r_scangle_other	3.491
r_mcangle_it	2.527
r_mcangle_other	2.525
r_scbond_it	2.196
r_scbond_other	2.194
r_angle_refined_deg	1.727
r_mcbond_it	1.678
r_mcbond_other	1.678
r_chiral_restr_other	0.761
r_angle_other_deg	0.593
r_nbd_refined	0.206
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.173
r_nbd_other	0.146
r_xyhbond_nbd_refined	0.136
r_symmetry_nbd_refined	0.082
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.068
r_symmetry_xyhbond_nbd_refined	0.031
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	939
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	43

Software

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