7B88 | pdb_00007b88

Crystal structure of Retinoic Acid Receptor alpha (RXRA) in complexed with S99 inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SJM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293.15	21% PEG 3350, 0.1 M Ammomium Acetate, 0.1 M tris 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.054	α = 90
b = 64.054	β = 90
c = 110.067	γ = 90

Symmetry
Space Group	P 43 21 2

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 EIGER2 X 16M		2019-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0000	SLS	X06SA

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	2.38	45.29	100	0.067	0.074	0.026	0.999	12.7	7.9		9753

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)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.38	2.51	100		0.933	1.061	0.365	0.733	2.1		8.3

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	6sjm	2.38	45.29	9267	439	99.93	0.2015	0.1988	0.2	0.2591	0.27	RANDOM	79.899

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]
1.12			1.12		-2.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.232
r_dihedral_angle_4_deg	21.202
r_dihedral_angle_3_deg	15.618
r_dihedral_angle_1_deg	6.277
r_angle_other_deg	1.161
r_angle_refined_deg	1.137
r_chiral_restr	0.058
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.232
r_dihedral_angle_4_deg	21.202
r_dihedral_angle_3_deg	15.618
r_dihedral_angle_1_deg	6.277
r_angle_other_deg	1.161
r_angle_refined_deg	1.137
r_chiral_restr	0.058
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1777
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	24

Software

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

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.