7Z9J

ATAD2 in complex with PepLite-Gly

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 Properties
Matthews coefficient	Solvent content
4.1	69.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.772	α = 90
b = 79.772	β = 90
c = 137.872	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		2019-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9116	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	1.9	48.8	100	0.259	0.266	0.058	0.999	14.3	38.9		21195

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	1.9	1.94			5.046	5.174	1.142	0.726		38.5

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	1.9	48.8	21134	1026	99.986	0.191	0.1891	0.2213	36.854

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]
-0.24	-0.12		-0.24		0.779

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.575
r_dihedral_angle_4_deg	18.211
r_dihedral_angle_3_deg	15.872
r_lrange_it	9.848
r_scangle_it	7.397
r_scbond_it	5.634
r_dihedral_angle_1_deg	5.18
r_mcangle_it	4.207
r_mcbond_it	3.188
r_angle_refined_deg	1.867

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.575
r_dihedral_angle_4_deg	18.211
r_dihedral_angle_3_deg	15.872
r_lrange_it	9.848
r_scangle_it	7.397
r_scbond_it	5.634
r_dihedral_angle_1_deg	5.18
r_mcangle_it	4.207
r_mcbond_it	3.188
r_angle_refined_deg	1.867
r_symmetry_nbd_refined	0.409
r_nbtor_refined	0.315
r_nbd_refined	0.229
r_xyhbond_nbd_refined	0.213
r_symmetry_xyhbond_nbd_refined	0.192
r_chiral_restr	0.119
r_bond_refined_d	0.013
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1084
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	42

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.