1Y9R | pdb_00001y9r

Crystal structure of the human mineralocorticoid receptor ligand-binding domain bound to deoxycorticosterone and harboring the S810L mutation responsible for a severe form of hypertension

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		3D HOMOLOGY MODEL OF THE HUMAN MINERALOCORTICOID RECEPTOR LIGAND BINDING DOMAIN CONSTRUCTED USING THE PROGESTERONE RECEPTOR LIGAND BINDING DOMAIN STRUCTURE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	297	PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.8	55.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.284	α = 90
b = 120.284	β = 90
c = 41.326	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	2003-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.979583	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	1.96	18.3	97.5	0.094	0.079	6.6	3	40302	40302			18.3

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		0.431	0.318	2.1	1.5	6049

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	3D HOMOLOGY MODEL OF THE HUMAN MINERALOCORTICOID RECEPTOR LIGAND BINDING DOMAIN CONSTRUCTED USING THE PROGESTERONE RECEPTOR LIGAND BINDING DOMAIN STRUCTURE	1.96	18.3	40302	40302	4101	84.1	0.241	0.2291	0.229	0.23	0.267	0.27	RANDOM	24.8

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]
0.694	0.3471		0.694		0.6881

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	19.8
c_scangle_it	2.07
c_mcangle_it	1.68
c_scbond_it	1.57
c_angle_deg	1.3
c_mcbond_it	1.09
c_improper_angle_d	0.9
c_bond_d	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3885
Nucleic Acid Atoms
Solvent Atoms	461
Heterogen Atoms	48

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
BEAST	model building
CNS	refinement
CCP4	data scaling
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.