7PX5 | pdb_00007px5

ATAD2 in complex with 1-Methyl-2-quinolone

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 BisTris pH 6-7, 1.7-2.1M Ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
4.08	69.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.507	α = 90
b = 79.507	β = 90
c = 138.224	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	IMAGE PLATE	MAR scanner 300 mm plate		2014-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54190

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	2.18	38.322	95.2	0.059	0.081	0.054	0.997	8.4	2.4		13347

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	2.18	38.29	95.2		0.016	0.022	0.015	0.999		2.2

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	2.18	38.322	13335	665	94.387	0.208	0.2064	0.21	0.2461	0.25	32.33

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]
0.042	0.021		0.042		-0.136

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.554
r_dihedral_angle_4_deg	18.563
r_dihedral_angle_3_deg	18.251
r_lrange_it	8.245
r_scangle_it	6.529
r_dihedral_angle_1_deg	5.841
r_scbond_it	4.348
r_mcangle_it	3.53
r_mcbond_it	2.491
r_angle_refined_deg	1.769

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.554
r_dihedral_angle_4_deg	18.563
r_dihedral_angle_3_deg	18.251
r_lrange_it	8.245
r_scangle_it	6.529
r_dihedral_angle_1_deg	5.841
r_scbond_it	4.348
r_mcangle_it	3.53
r_mcbond_it	2.491
r_angle_refined_deg	1.769
r_nbtor_refined	0.327
r_symmetry_nbd_refined	0.282
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.181
r_chiral_restr	0.118
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1069
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
XDS	data reduction
Aimless	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.