3JVM | pdb_00003jvm

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, soaked with 10 mM H3-K(ac)14 octapeptide GGK(ac)APRKQ, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.1	α = 90
b = 73.15	β = 90
c = 32.16	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		2008-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97886	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	95.2	0.066	23.39		37336	37336	-3	-3	15.484

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	96.3		0.577	6.9

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 2OUO	1.2	19.53	37326	37326	1846	95.17	0.118	0.117	0.116	0.12	0.151	0.15	RANDOM	10.513

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]
1.08			0.12		-1.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.71
r_dihedral_angle_4_deg	23.395
r_sphericity_free	16.08
r_dihedral_angle_3_deg	10.514
r_sphericity_bonded	7.222
r_scangle_it	6.186
r_dihedral_angle_1_deg	6.082
r_scbond_it	5.091
r_mcangle_it	3.587
r_mcbond_it	2.994
r_rigid_bond_restr	2.908
r_angle_refined_deg	2.366
r_mcbond_other	1.423
r_angle_other_deg	1.245
r_symmetry_vdw_other	0.38
r_xyhbond_nbd_refined	0.323
r_nbd_refined	0.32
r_symmetry_vdw_refined	0.285
r_symmetry_hbond_refined	0.247
r_nbd_other	0.202
r_nbtor_refined	0.2
r_chiral_restr	0.152
r_nbtor_other	0.104
r_bond_refined_d	0.034
r_gen_planes_refined	0.015
r_gen_planes_other	0.005
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	950
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	20

Software

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