9DU7 | pdb_00009du7

KEAP1 BTB domain in complex with the covalent activator VVD-065

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4CXI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.2	293.15	24% PEG 3350, 100 mM CHES pH 9.2

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.737	α = 90
b = 72.737	β = 90
c = 64.209	γ = 90

Symmetry
Space Group	P 43

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		2021-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.000030	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.867	48.183	98.21	0.0625	0.06795	0.02625	0.998	15.21	6.9		27387			42.64

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.87	1.937			0.525

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.867	48.183	27387	1336	98.144	0.194	0.1915	0.1993	0.2314	0.2389	44.499

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]
-0.466			-0.466		0.933

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.115
r_dihedral_angle_3_deg	15.21
r_lrange_it	9.482
r_lrange_other	9.437
r_scangle_it	7.957
r_scangle_other	7.954
r_dihedral_angle_1_deg	5.918
r_scbond_it	5.497
r_scbond_other	5.495
r_mcangle_it	5.464
r_mcangle_other	5.461
r_dihedral_angle_2_deg	5.458
r_mcbond_it	4.158
r_mcbond_other	4.158
r_angle_refined_deg	1.589
r_angle_other_deg	0.532
r_nbd_refined	0.218
r_symmetry_nbd_other	0.198
r_nbd_other	0.198
r_nbtor_refined	0.188
r_symmetry_xyhbond_nbd_refined	0.158
r_xyhbond_nbd_refined	0.151
r_symmetry_nbd_refined	0.124
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.079
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1974
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing