8CHP | pdb_00008chp

The FK1 domain of FKBP51 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophenyl)sulfinyl)-3-(pyridin-2-ylmethyl)-5-vinyl-3,10-diazabicyclo[4.3.1]decan-2-one

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OBK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	32% PEG3350, 0.2 M ammonium acetate, 0.1M HEPES-NaOH pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.306	α = 90
b = 54.452	β = 90
c = 56.405	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		2022-09-10	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	42.31	100	0.031	0.037	0.019	1	26.3	7		71074

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	1.02			0.363	0.43	0.226	0.923		6.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1	28.761	71000	3442	99.931	0.176	0.1751	0.18	0.1871	0.2	9.241

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]
0.012			0.091		-0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.631
r_dihedral_angle_3_deg	11.403
r_dihedral_angle_1_deg	7.495
r_dihedral_angle_2_deg	5.681
r_lrange_it	5.183
r_lrange_other	4.845
r_scangle_it	2.472
r_scangle_other	2.47
r_chiral_restr_other	2.145
r_angle_refined_deg	1.903
r_scbond_it	1.632
r_scbond_other	1.631
r_mcangle_it	1.31
r_mcangle_other	1.309
r_mcbond_it	0.912
r_mcbond_other	0.91
r_angle_other_deg	0.869
r_symmetry_xyhbond_nbd_refined	0.235
r_xyhbond_nbd_refined	0.23
r_nbd_refined	0.201
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.184
r_nbd_other	0.165
r_symmetry_nbd_refined	0.145
r_chiral_restr	0.134
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	961
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	30

Software

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