2ABI | pdb_00002abi

Crystal structure of the human mineralocorticoid receptor ligand-binding domain bound to deoxycorticosterone

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y9R	PDB 1Y9R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.1	297	PEG4000, HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.02	19.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.77	α = 90
b = 119.77	β = 90
c = 41.5	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	69	CCD	MARRESEARCH	MIRRORS	2004-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.979870	ESRF	BM30A

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	2.33	39.2	87.5	0.147	0.08	10.52	3.192	28454	27439

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)
	1.96	2.07	86.4		0.662	0.636	1.7	2.03	3846

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 1Y9R	2.33	39.2	28659	24920	2519	87.5	0.228	0.2074	0.2074	0.2	0.2639	0.25	RANDOM	44.5

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]
-2.45	2.29		-2.45		4.91

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	19.3
c_scangle_it	2.35
c_mcangle_it	1.79
c_scbond_it	1.58
c_angle_deg	1.2
c_mcbond_it	1.08
c_improper_angle_d	0.75
c_bond_d	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5622
Nucleic Acid Atoms
Solvent Atoms	381
Heterogen Atoms	72

Software

Software
Software Name	Purpose
XDS	data scaling
XDS	data reduction
BEAST	model building
CNS	refinement
BEAST	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.