4QUU | pdb_00004quu

Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) complexed with Histone H4-K(ac)5

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DAI	pdb id: 3DAI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277.15	apo crystals grew in 1.8-2.2 M ammonium sulphate, 0.1 M Bis-Tris, pH 5.5-6.5. Soaking performed in 28-32% PEG 3350, 50 mM bis-tris pH 5.5, 50 mM ammonium phosphate and 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
3.73	67.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.201	α = 90
b = 79.201	β = 90
c = 139.141	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	RIGAKU RAXIS IV		2012-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	34.44	100	0.09	16.2	9.7	24588	24527			26.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	100		0.894	2.4	9.9	3483

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	pdb id: 3DAI	1.8	34.42	2	24527	23271	1255	99.86	0.202	0.17037	0.16881	0.18	0.2004	0.21	RANDOM	29.089

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	0.02		0.02		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.399
r_dihedral_angle_4_deg	19.111
r_dihedral_angle_3_deg	12.526
r_long_range_B_other	9.738
r_long_range_B_refined	9.737
r_dihedral_angle_1_deg	4.424
r_scangle_other	3.5
r_scbond_it	2.349
r_scbond_other	2.335
r_mcangle_other	1.841
r_mcangle_it	1.833
r_angle_refined_deg	1.528
r_mcbond_it	1.218
r_mcbond_other	1.209
r_angle_other_deg	0.82
r_chiral_restr	0.099
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1119
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	41

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling