3MUK | pdb_00003muk

Crystal structure of Brd4 bromodomain 1 with propionylated histone H3-K(prop)23

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3JVJ	PDB ENTRY 3JVJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	3.6M Na formate, 10% glycerol, soaked with 20-times excess of histone octapeptide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.213	α = 90
b = 47.008	β = 90
c = 78.101	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		2009-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00	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	1.75	19.6	99.7	0.086	20.1		13605	13605	-3	-3

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)
	1.75	1.8	100		0.532	4.2		1072

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 (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 3JVJ	1.75	19.6	12865	12865	730	99.76	0.17451	0.17206	0.19	0.21879	0.23	RANDOM	29.685

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]
4.84			-2.41		-2.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.433
r_dihedral_angle_3_deg	13.147
r_dihedral_angle_4_deg	12.363
r_dihedral_angle_1_deg	6.144
r_scangle_it	3.7
r_scbond_it	2.781
r_angle_refined_deg	1.936
r_mcangle_it	1.79
r_mcbond_it	1.226
r_angle_other_deg	1.051
r_mcbond_other	0.375
r_xyhbond_nbd_refined	0.316
r_symmetry_hbond_refined	0.259
r_nbd_refined	0.232
r_symmetry_vdw_other	0.202
r_nbtor_refined	0.2
r_symmetry_vdw_refined	0.195
r_nbd_other	0.184
r_chiral_restr	0.116
r_nbtor_other	0.102
r_bond_refined_d	0.023
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1067
Nucleic Acid Atoms
Solvent Atoms	151
Heterogen Atoms	4

Software

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