4DRP | pdb_00004drp

Evaluation of Synthetic FK506 Analogs as Ligands for the FK506-Binding Proteins 51 and 52: Complex of FKBP51 with 2-(3-((R)-3-(3,4-dimethoxyphenyl)-1-((S)-1-(2-((1R,2S)-2-ethyl-1-hydroxy-cyclohexyl)-2-oxoacetyl)piperidine-2-carbonyloxy)propyl)phenoxy)acetic acid from cocrystallization

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	293	37.5 % PEG3350, 0.1 M NH4OAc, 0.1 M HEPES pH 7.5, 10 % DMSO, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.913	α = 90
b = 56.563	β = 90
c = 57.589	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	CCD	ADSC QUANTUM 315r		2010-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.900	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.792	25.386	97.5	0.062	0.062	12.4	3.3	15448	15448			20.88

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.89	84		0.19	0.19	3.9	2.3	1862

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRY 3O5Q	1.8	20	14853	14559	769	98.02	0.2221	0.2221	0.22	0.23	0.2609	0.27	RANDOM	20.0242

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]
0.14			-0.09		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.48
r_dihedral_angle_4_deg	18.585
r_dihedral_angle_3_deg	11.543
r_dihedral_angle_1_deg	6.547
r_scangle_it	2.927
r_scbond_it	1.876
r_angle_refined_deg	1.472
r_mcangle_it	1.164
r_mcbond_it	0.68
r_chiral_restr	0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.48
r_dihedral_angle_4_deg	18.585
r_dihedral_angle_3_deg	11.543
r_dihedral_angle_1_deg	6.547
r_scangle_it	2.927
r_scbond_it	1.876
r_angle_refined_deg	1.472
r_mcangle_it	1.164
r_mcbond_it	0.68
r_chiral_restr	0.1
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	986
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	46

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling

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.