2NXB

Crystal structure of human Bromodomain containing protein 3 (BRD3)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X0J	pdb entry 1X0J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.20M KSCN, 0.1M BTPop, 20% PEG3350, 10% EtGly, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.504	α = 90
b = 61.84	β = 90
c = 84.523	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 225 mm CCD		2006-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

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	1.4	50	100	0.084	0.084	10.2	6.1	54074	54074

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	1.4	1.45	100		0.398	0.398		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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1X0J	1.4	49.94	54073	51261	2748	99.88	0.16848	0.16761	0.18479	RANDOM	17.171

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]
0.86			-0.29		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.037
r_dihedral_angle_4_deg	12.234
r_dihedral_angle_3_deg	11.448
r_dihedral_angle_1_deg	4.921
r_scangle_it	2.489
r_angle_other_deg	2.091
r_scbond_it	1.668
r_angle_refined_deg	1.256
r_mcangle_it	0.962
r_mcbond_it	0.543
r_symmetry_vdw_refined	0.254
r_nbd_refined	0.222
r_symmetry_vdw_other	0.199
r_nbtor_refined	0.195
r_nbd_other	0.174
r_symmetry_hbond_refined	0.171
r_mcbond_other	0.159
r_xyhbond_nbd_refined	0.144
r_nbtor_other	0.09
r_chiral_restr	0.071
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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	1899
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms	29

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling