3JVL

Crystal structure of bromodomain 2 of mouse Brd4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OUO	PDB ENTRY 2OUO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	0.1M Tris/HCl, 25% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.06	α = 90
b = 73.05	β = 90
c = 32.3	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		2008-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97642	SLS	X10SA

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	1.2	19.53	99.9	0.043	20.37		39272	39272	-3	-3	14.483

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)
	1.2	1.25	100		0.381	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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2OUO	1.2	19.53	39262	39262	1927	99.88	0.118	0.117	0.116	0.145	RANDOM	10.389

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]
0.59			0.85		-1.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.973
r_sphericity_free	18.774
r_dihedral_angle_4_deg	15.468
r_dihedral_angle_3_deg	12.175
r_sphericity_bonded	8.946
r_dihedral_angle_1_deg	6.708
r_scangle_it	6.304
r_scbond_it	5.121
r_mcangle_it	3.436
r_rigid_bond_restr	3.074
r_mcbond_it	2.921
r_angle_refined_deg	2.551
r_mcbond_other	1.517
r_angle_other_deg	1.248
r_xyhbond_nbd_refined	0.368
r_nbd_refined	0.322
r_symmetry_vdw_refined	0.288
r_symmetry_hbond_refined	0.288
r_symmetry_vdw_other	0.27
r_nbd_other	0.211
r_nbtor_refined	0.206
r_chiral_restr	0.156
r_nbtor_other	0.104
r_bond_refined_d	0.031
r_gen_planes_refined	0.014
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	987
Nucleic Acid Atoms
Solvent Atoms	219
Heterogen Atoms	24

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
MOLREP	phasing