7Z9N

ATAD2 in complex with PepLite-Val

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DAI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.158	α = 90
b = 79.158	β = 90
c = 138.043	γ = 120

Symmetry
Space Group	P 65 2 2

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		2019-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9762	Diamond	I04-1

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	1.34	61.4	98.4	0.047	0.049	0.015	0.998	27.9	18.2		56991

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.34	1.36			1.734	2.049	1.068	0.375		6

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3DAI	1.34	48.686	56917	2822	98.141	0.209	0.2078	0.227	30.216

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]
0.129	0.065		0.129		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.7
r_dihedral_angle_4_deg	15.868
r_dihedral_angle_3_deg	13.546
r_lrange_it	9.529
r_scangle_it	7.993
r_scbond_it	5.727
r_dihedral_angle_1_deg	4.606
r_mcangle_it	3.622
r_angle_refined_deg	2.601
r_mcbond_it	2.447

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.7
r_dihedral_angle_4_deg	15.868
r_dihedral_angle_3_deg	13.546
r_lrange_it	9.529
r_scangle_it	7.993
r_scbond_it	5.727
r_dihedral_angle_1_deg	4.606
r_mcangle_it	3.622
r_angle_refined_deg	2.601
r_mcbond_it	2.447
r_symmetry_xyhbond_nbd_refined	0.393
r_nbtor_refined	0.325
r_nbd_refined	0.226
r_xyhbond_nbd_refined	0.217
r_symmetry_nbd_refined	0.198
r_chiral_restr	0.129
r_bond_refined_d	0.023
r_gen_planes_refined	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1084
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
PHASER	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.