4FLP | pdb_00004flp

Crystal Structure of the first bromodomain of human BRDT in complex with the inhibitor JQ1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2RFJ	Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	2OSS	Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	2OUO	Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	2GRC	Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	2OO1	Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	3DAI	Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	3D7C	Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	3DWY	Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	0.1M BisTris propane pH 8.0, 0.15M KSCN, 25% PEG3350, 10% EtGly , VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.4	α = 90
b = 57.42	β = 90
c = 128.69	γ = 90

Symmetry
Space Group	P 21 2 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	ADSC QUANTUM 315r		2011-01-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	2.2	37.4	99.5	0.11	0.11	7.2	3.4	14729	14655

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	99.9		0.655	0.655	1.1	3.6

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	Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY	2.23	42.84	14168	13419	708	99.71	0.21343	0.21113	0.21	0.25487	0.26	RANDOM	37.929

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]
0.42			-0.49		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.596
r_dihedral_angle_3_deg	18.006
r_scangle_it	11.799
r_dihedral_angle_4_deg	11.536
r_scbond_it	9.847
r_mcangle_it	6.335
r_dihedral_angle_1_deg	5.893
r_mcbond_it	4.17
r_angle_refined_deg	1.66
r_mcbond_other	1.259
r_angle_other_deg	0.923
r_chiral_restr	0.086
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1730
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	63

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
MOSFLM	data reduction