6EU9 | pdb_00006eu9

Crystal structure of Platynereis dumerilii RAR ligand-binding domain in complex with all-trans retinoic acid

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2 M sodium acetate, 0.1 M HEPES pH 7.5, 20% PEG 3000

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 187.41	α = 90
b = 68.15	β = 100.75
c = 95.08	γ = 90

Symmetry
Space Group	C 1 2 1

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		2013-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.0	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	2.69	50	98.8	0.053	0.064	0.035	17.6	3.2		32596

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	2.69	2.78	99.7		0.589	0.589	0.697	0.369	1.3	3.5

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.69	50	30964	1633	98.58	0.2573	0.2551	0.26	0.2997	0.31	RANDOM	52.951

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]
2.17		-2.29	-2.2		0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.542
r_dihedral_angle_4_deg	28.434
r_dihedral_angle_3_deg	25.517
r_dihedral_angle_1_deg	7.216
r_angle_refined_deg	2.23
r_chiral_restr	0.146
r_bond_refined_d	0.019
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7069
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	44

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MoRDa	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.