3LXJ | pdb_00003lxj

Crystal Structure of the Bromodomain of Human AAA domain containing 2B (ATAD2B)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DAI	ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY
experimental model	PDB	2NXB	ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY
experimental model	PDB	2OO1	ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY
experimental model	PDB	2OSS	ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY
experimental model	PDB	2OUO	ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY
experimental model	PDB	2RFJ	ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY
experimental model	PDB	3HMH	ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY
experimental model	PDB	3D7C	ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY
experimental model	PDB	3DWY	ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	20% isopropanol 0.1M tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.64	α = 90
b = 79.64	β = 90
c = 204.051	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2009-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9204	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.327	40.81	99.3	0.08	0.08	10.8	4.9	31225	31006

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.34	2.46	99.6		0.653	0.653	2	4.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY	2.33	40.81	31012	29113	1586	98.99	0.21405	0.21206	0.2024	0.2534	0.2327	RANDOM	45.949

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]
6.62			6.62		-13.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.432
r_dihedral_angle_3_deg	15.461
r_dihedral_angle_4_deg	15.132
r_scangle_it	6.558
r_scbond_it	6.334
r_dihedral_angle_1_deg	5.799
r_mcangle_it	3.906
r_mcbond_it	2.856
r_angle_refined_deg	1.307
r_mcbond_other	1.21
r_angle_other_deg	0.865
r_chiral_restr	0.069
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4268
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	20

Software

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