7R0Y | pdb_00007r0y

ATAD2 in complex with PepLite-Glu

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 = 79.288	α = 90
b = 79.288	β = 90
c = 138.015	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	0.976	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	1.43	61.48	99.5	0.086	0.091	0.027	0.999	17.3	19.5		47816

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	1.43	1.45			2.943	3.252	1.353	0.195		10.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3DAI	1.43	61.48	47744	2335	99.34	0.196	0.1951	0.1952	0.2135	0.2135	34.361

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]
0.162	0.081		0.162		-0.526

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.342
r_dihedral_angle_3_deg	15.232
r_dihedral_angle_4_deg	14.137
r_lrange_it	12.973
r_scangle_it	9.067
r_scbond_it	6.192
r_dihedral_angle_1_deg	4.547
r_mcangle_it	4.385
r_mcbond_it	3.024
r_angle_refined_deg	2.633

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.342
r_dihedral_angle_3_deg	15.232
r_dihedral_angle_4_deg	14.137
r_lrange_it	12.973
r_scangle_it	9.067
r_scbond_it	6.192
r_dihedral_angle_1_deg	4.547
r_mcangle_it	4.385
r_mcbond_it	3.024
r_angle_refined_deg	2.633
r_symmetry_nbd_refined	0.639
r_symmetry_xyhbond_nbd_refined	0.498
r_nbtor_refined	0.321
r_xyhbond_nbd_refined	0.319
r_nbd_refined	0.233
r_chiral_restr	0.151
r_bond_refined_d	0.019
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1084
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	35

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.