6SAF | pdb_00006saf

The Fk1 domain of FKBP51 in complex with (S)-(R)-3-(3,4-dimethoxyphenyl)-1-(3-(2-morpholinoethoxy)phenyl)propyl 1-((1R,4aR,8aR)-4-oxodecahydronaphthalene-1-carbonyl)piperidine-2-carboxylate

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	28 % PEG-3350, 0.2 M NH4-acetate and 0.1 M HEPES-NaOH pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.555	α = 90
b = 50.334	β = 90
c = 62.776	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	2.05	39.27	99.7	0.065	0.072	0.031	13.3	5.3	8890	8890			34

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	2.05	2.16	99.6		0.597	0.597	0.66	0.278	1.3	5.4

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	2.05	30	8428	423	99.52	0.194	0.1903	0.2	0.2731	0.28	RANDOM	48.131

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]
3.96			-2.68		-1.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.4
r_dihedral_angle_4_deg	15.008
r_dihedral_angle_3_deg	14.372
r_dihedral_angle_1_deg	7.571
r_angle_refined_deg	1.857
r_angle_other_deg	1.45
r_chiral_restr	0.088
r_bond_refined_d	0.014
r_bond_other_d	0.008
r_gen_planes_refined	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.4
r_dihedral_angle_4_deg	15.008
r_dihedral_angle_3_deg	14.372
r_dihedral_angle_1_deg	7.571
r_angle_refined_deg	1.857
r_angle_other_deg	1.45
r_chiral_restr	0.088
r_bond_refined_d	0.014
r_bond_other_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	979
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	50

Software

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

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.