4TT4 | pdb_00004tt4

Crystal structure of ATAD2A bromodomain complexed with H3(1-21)K14Ac peptide

X-RAY DIFFRACTION

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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, SITTING DROP	8.5	278	2.0M Ammonium sulfate, 100mM Tris pH8.5.

Crystal Properties
Matthews coefficient	Solvent content
3.86	68.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.16	α = 90
b = 115.68	β = 90
c = 77.5	γ = 90

Symmetry
Space Group	C 2 2 21

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	2.7	57.84	99.9	0.2	0.084	0.992	6	6.7		13680

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	2.7	2.83	100		0.818	0.335	0.89	2.2	7	1790

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	2.7	79.01	13654	681	99.7	0.2161	0.2149	0.23	0.2404	0.25	RANDOM	32.511

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]
-0.53			0.01		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.775
r_dihedral_angle_3_deg	14.56
r_dihedral_angle_4_deg	14.307
r_dihedral_angle_1_deg	4.533
r_mcangle_it	2.736
r_mcbond_it	1.707
r_mcbond_other	1.701
r_angle_refined_deg	1.215
r_angle_other_deg	1.045
r_chiral_restr	0.123
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2201
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	34

Software

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