6L88

Crystal structure of mineralocorticoid receptor ligand binding domain in complex with esaxerenone

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	2.0-2.5 M sodium nitrate, 0.1 M Tris-HCl pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.888	α = 90
b = 160.888	β = 90
c = 160.888	γ = 90

Symmetry
Space Group	P 21 3

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 2M		2018-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.000	Photon Factory	AR-NE3A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	3	19.96	99.8	0.397	0.417	0.998	5.42	10.303		27958			93.301

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.19	99.7		6.61	7.001	0.101	0.34	9.258

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5mwp	3	19.96	26335	1441	99.39	0.2705	0.2685	0.307	RANDOM	116.551

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.621
r_dihedral_angle_3_deg	20.48
r_dihedral_angle_4_deg	12.311
r_dihedral_angle_1_deg	7.538
r_angle_refined_deg	1.61
r_angle_other_deg	1.173
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.621
r_dihedral_angle_3_deg	20.48
r_dihedral_angle_4_deg	12.311
r_dihedral_angle_1_deg	7.538
r_angle_refined_deg	1.61
r_angle_other_deg	1.173
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6084
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	128

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.