2DYH

Crystal structure of the Keap1 protein in complexed with the N-terminal region of the Nrf2 transcription factor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X2J	PDB ENTRY 1X2J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	298	Ammonium sulfate, Lithium Sulfate, Sodium Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.131	α = 90
b = 103.131	β = 90
c = 56.141	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	103	IMAGE PLATE	RIGAKU RAXIS IV++	mirrors	2005-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.9	50	98.2	0.086		8.6	27043	26542		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.97	88		0.398		3.6	2359

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	PDB ENTRY 1X2J	1.9	20	25143	1335	98.2	0.17432	0.17237	0.21102	RANDOM	34.302

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]
-0.8	-0.4		-0.8		1.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.524
r_dihedral_angle_4_deg	19.811
r_dihedral_angle_3_deg	13.53
r_dihedral_angle_1_deg	7.018
r_scangle_it	3.81
r_scbond_it	2.691
r_mcangle_it	1.808
r_angle_refined_deg	1.55
r_mcbond_it	1.142
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.524
r_dihedral_angle_4_deg	19.811
r_dihedral_angle_3_deg	13.53
r_dihedral_angle_1_deg	7.018
r_scangle_it	3.81
r_scbond_it	2.691
r_mcangle_it	1.808
r_angle_refined_deg	1.55
r_mcbond_it	1.142
r_nbtor_refined	0.304
r_nbd_refined	0.221
r_symmetry_vdw_refined	0.218
r_symmetry_hbond_refined	0.171
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.118
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2321
Nucleic Acid Atoms
Solvent Atoms	307
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
DNA	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	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.