7Z9H | pdb_00007z9h

ATAD2 in complex with PepLite-Asp

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, SITTING DROP	6.5	293	0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.145	α = 90
b = 79.145	β = 90
c = 137.536	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	68.54	99.3	0.047	0.05	0.015	1	24.9	17.3		57366

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			1.564	1.898	1.053	0.296		5.2

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	1.34	68.54	57288	2981	99.195	0.211	0.2099	0.21	0.2269	0.23	31.198

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]
0.159	0.08		0.159		-0.517

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.089
r_dihedral_angle_3_deg	14.49
r_dihedral_angle_4_deg	14.009
r_lrange_it	11.934
r_scangle_it	8.137
r_scbond_it	5.628
r_dihedral_angle_1_deg	4.367
r_mcangle_it	3.711
r_mcbond_it	2.529
r_angle_refined_deg	2.264

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.089
r_dihedral_angle_3_deg	14.49
r_dihedral_angle_4_deg	14.009
r_lrange_it	11.934
r_scangle_it	8.137
r_scbond_it	5.628
r_dihedral_angle_1_deg	4.367
r_mcangle_it	3.711
r_mcbond_it	2.529
r_angle_refined_deg	2.264
r_nbtor_refined	0.322
r_symmetry_xyhbond_nbd_refined	0.29
r_nbd_refined	0.238
r_xyhbond_nbd_refined	0.217
r_symmetry_nbd_refined	0.19
r_chiral_restr	0.127
r_bond_refined_d	0.014
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1084
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	43

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.