2OO1 | pdb_00002oo1

Crystal structure of the Bromo domain 2 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	7.5	277	0.2M NaF, 0.1M BTProp, 20% PEG3350, 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.837	α = 90
b = 64.678	β = 90
c = 91.827	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	MARMOSAIC 225 mm CCD		2006-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97910	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	1.7	50	99.7	0.094	0.094	6.6	4.9	69322	69114

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.76	100			4.1	6853

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 (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 entry 1X0J	1.7	50	69114	3417	99.7	0.187	0.187	0.186	0.2	0.213	0.22	RANDOM	20.332

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]
1.38			-0.81		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.52
r_dihedral_angle_4_deg	21.482
r_dihedral_angle_3_deg	11.802
r_dihedral_angle_1_deg	4.874
r_scangle_it	4.77
r_scbond_it	3.053
r_mcangle_it	2.032
r_angle_refined_deg	1.749
r_mcbond_it	1.159
r_angle_other_deg	1.01
r_mcbond_other	0.357
r_symmetry_vdw_other	0.257
r_nbd_refined	0.228
r_symmetry_hbond_refined	0.225
r_nbd_other	0.206
r_symmetry_vdw_refined	0.201
r_nbtor_refined	0.193
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.107
r_nbtor_other	0.092
r_bond_refined_d	0.021
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3573
Nucleic Acid Atoms
Solvent Atoms	475
Heterogen Atoms	48

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