5OBK | pdb_00005obk

The Fk1 domain of FKBP51 in complex with (1S,5S,6R)-10-((3,5-dichlorophenyl)sulfonyl)-5-(hydroxymethyl)-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3O5Q	pdbid 3O5Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	30 % PEG-3350, 0.2 M NH4-acetate and 0.1 M HEPES-NaOH pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.819	α = 90
b = 54.915	β = 90
c = 56.745	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 PILATUS 6M		2015-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97857	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	0.94	39.462	95.4	0.04	0.045	0.021	17.6	3.9		68012

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1	1.05	74.7		0.292	0.292	0.362	0.208	2.6	2.2

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdbid 3O5Q	1	30	64500	3434	95.36	0.1198	0.119	0.12	0.1356	0.14	RANDOM	14.554

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]
-0.45			-0.2		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	29.378
r_dihedral_angle_2_deg	27.729
r_dihedral_angle_4_deg	23.861
r_dihedral_angle_3_deg	14.616
r_sphericity_bonded	10.37
r_dihedral_angle_1_deg	6.958
r_rigid_bond_restr	2.989
r_angle_refined_deg	1.79
r_angle_other_deg	0.969
r_chiral_restr	0.175

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	29.378
r_dihedral_angle_2_deg	27.729
r_dihedral_angle_4_deg	23.861
r_dihedral_angle_3_deg	14.616
r_sphericity_bonded	10.37
r_dihedral_angle_1_deg	6.958
r_rigid_bond_restr	2.989
r_angle_refined_deg	1.79
r_angle_other_deg	0.969
r_chiral_restr	0.175
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	982
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms	33

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
TRUNCATE	data scaling
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.