5QXS | pdb_00005qxs

PanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with DF852

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	1.6M Ammonium Sulfate, 0.1M bis-tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
4.21	70.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.52	α = 90
b = 80.52	β = 90
c = 139.43	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		2016-04-23		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	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	1.62	69.73	100	0.132	0.135	0.031	1	17.9	19		34760

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	1.62	1.66	100		2.182	2.241	0.507	0.517		19.3	2500

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	3DAI	1.62	69.73	32959	1736	99.93	0.1746	0.1735	0.21	0.1963	0.22	RANDOM	31.562

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]
-0.02	-0.01		-0.02		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.477
r_dihedral_angle_4_deg	15.381
r_dihedral_angle_3_deg	14.259
r_dihedral_angle_1_deg	4.504
r_mcangle_it	3.262
r_mcbond_other	1.886
r_mcbond_it	1.868
r_angle_refined_deg	1.756
r_angle_other_deg	1.416
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.477
r_dihedral_angle_4_deg	15.381
r_dihedral_angle_3_deg	14.259
r_dihedral_angle_1_deg	4.504
r_mcangle_it	3.262
r_mcbond_other	1.886
r_mcbond_it	1.868
r_angle_refined_deg	1.756
r_angle_other_deg	1.416
r_chiral_restr	0.095
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1084
Nucleic Acid Atoms
Solvent Atoms	217
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	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.