7QZZ | pdb_00007qzz

ATAD2 in complex with FragLite31

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
4.04	69.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.257	α = 90
b = 79.257	β = 90
c = 137.706	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		2019-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.898	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	2.52	68.85	100	0.7	0.717	0.156	0.959	10.7	37.8		9241

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.52	2.62			11.298	2.444	0.463		38.8

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	2.52	68.733	9196	434	100	0.205	0.2031	0.2	0.2399	0.24	62.564

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]
-1.145	-0.572		-1.145		3.713

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.769
r_dihedral_angle_3_deg	16.57
r_dihedral_angle_4_deg	14.339
r_lrange_it	13.918
r_scangle_it	11.061
r_scbond_it	8.08
r_mcangle_it	7.216
r_dihedral_angle_1_deg	5.454
r_mcbond_it	5.048
r_angle_refined_deg	1.677

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.769
r_dihedral_angle_3_deg	16.57
r_dihedral_angle_4_deg	14.339
r_lrange_it	13.918
r_scangle_it	11.061
r_scbond_it	8.08
r_mcangle_it	7.216
r_dihedral_angle_1_deg	5.454
r_mcbond_it	5.048
r_angle_refined_deg	1.677
r_nbtor_refined	0.329
r_nbd_refined	0.251
r_xyhbond_nbd_refined	0.243
r_symmetry_nbd_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.147
r_chiral_restr	0.12
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1084
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	45

Software

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