7PPX | pdb_00007ppx

ATAD2 in complex with FragLite3

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		293	0.1M HEPES pH 7.0, 2.4 AmSO4, ATAD2~5 mg mL-1.

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.205	α = 90
b = 79.205	β = 90
c = 137.91	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		2019-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.97959	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	1.35	68.96	99.7	0.055	0.058	0.017	1	22.9	19.8		56615

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	1.35	1.37			3.9	4.317	1.813	0.204		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	1.35	68.688	56534	2936	99.607	0.212	0.2108	0.21	0.2306	0.23	32.546

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]
0.024	0.012		0.024		-0.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.235
r_dihedral_angle_4_deg	18.919
r_dihedral_angle_3_deg	17.038
r_lrange_it	11.505
r_scangle_it	8.356
r_scbond_it	5.761
r_dihedral_angle_1_deg	4.558
r_mcangle_it	3.992
r_mcbond_it	2.817
r_angle_refined_deg	2.247

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.235
r_dihedral_angle_4_deg	18.919
r_dihedral_angle_3_deg	17.038
r_lrange_it	11.505
r_scangle_it	8.356
r_scbond_it	5.761
r_dihedral_angle_1_deg	4.558
r_mcangle_it	3.992
r_mcbond_it	2.817
r_angle_refined_deg	2.247
r_nbtor_refined	0.319
r_symmetry_xyhbond_nbd_refined	0.234
r_nbd_refined	0.227
r_xyhbond_nbd_refined	0.19
r_symmetry_nbd_refined	0.177
r_chiral_restr	0.137
r_bond_refined_d	0.016
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1084
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	65

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
pointless	data scaling
DIALS	data collection
DIMPLE	phasing
Coot	model building
DIALS	data reduction

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.