4TTE | pdb_00004tte

Crystal structure of ATAD2A bromodomain complexed with methyl 3-amino-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzoate

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	5.5	298	2.1-2.4M Ammonium Sulfate, 0.1M Bis-Tris pH5.5, 10% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
4.04	69.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.31	α = 90
b = 79.31	β = 90
c = 137.381	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	193	CCD	ADSC QUANTUM 315r		2013-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11587	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.8	48.57	100	0.083	0.018	0.999	25	21.2		24459

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84	100		0.98	0.28	0.804	2.5	13	1411

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	MOLECULAR REPLACEMENT	THROUGHOUT	3DAI	1.8	68.68	24396	1244	99.96	0.184	0.1833	0.19	0.197	0.2	RANDOM	30.077

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]
					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.521
r_dihedral_angle_4_deg	14.334
r_dihedral_angle_3_deg	13.296
r_dihedral_angle_1_deg	4.329
r_mcangle_it	2.975
r_mcbond_it	1.954
r_mcbond_other	1.946
r_angle_refined_deg	1.482
r_angle_other_deg	0.844
r_chiral_restr	0.089

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.521
r_dihedral_angle_4_deg	14.334
r_dihedral_angle_3_deg	13.296
r_dihedral_angle_1_deg	4.329
r_mcangle_it	2.975
r_mcbond_it	1.954
r_mcbond_other	1.946
r_angle_refined_deg	1.482
r_angle_other_deg	0.844
r_chiral_restr	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1084
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction

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.