2OUO | pdb_00002ouo

Crystal Structure of the Bromo domain 2 in human Bromodomain Containing Protein 4 (BRD4)

X-RAY DIFFRACTION

---

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	277	0.1M MIB, 30% PEG 1000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.032	α = 90
b = 73.698	β = 90
c = 33.467	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	IMAGE PLATE	RIGAKU RAXIS		2007-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54000

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	1.74	73.72	99.3	0.065	0.065	11.4	3.7	15125	15125

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	1.74	1.78	98.6		0.618		3.3	1156

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 (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	1.89	50	12030	12030	722	98.16	0.184	0.184	0.182	0.18	0.216	0.21	RANDOM	27.303

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]
-0.26			0.18		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.577
r_dihedral_angle_4_deg	26.097
r_dihedral_angle_3_deg	11.279
r_dihedral_angle_1_deg	5.308
r_scangle_it	2.936
r_scbond_it	2.144
r_angle_refined_deg	1.531
r_mcangle_it	1.455
r_mcbond_it	1.053
r_angle_other_deg	1.048
r_mcbond_other	0.316
r_symmetry_vdw_other	0.292
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.215
r_nbd_other	0.183
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.153
r_symmetry_hbond_refined	0.139
r_chiral_restr	0.09
r_nbtor_other	0.089
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	882
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	12

Software

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