5BT5

Crystal structure of BRD2 second bromodomain in complex with SGC-CBP30 chemical probe

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.2 M sodium/potassium tartrate, 20% PEG 3350, 10% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.761	α = 90
b = 71.806	β = 90
c = 31.996	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	PIXEL	DECTRIS PILATUS 6M		2014-06-07	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	1.4	42.52	99.3	0.079	0.027	22.3	9.2	224988	24507			5.314

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	1.4	1.48	95.9		0.165	11.6	7.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.4	42.52	23265	1203	99.18	0.16078	0.1597	0.18204	RANDOM	11.732

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]
0.01			-0.24		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.945
r_dihedral_angle_4_deg	23.617
r_dihedral_angle_3_deg	11.239
r_long_range_B_refined	5.048
r_dihedral_angle_1_deg	4.867
r_long_range_B_other	4.722
r_scangle_other	2.256
r_angle_refined_deg	1.565
r_scbond_it	1.372
r_scbond_other	1.371
r_mcangle_other	1.347
r_mcangle_it	1.343
r_angle_other_deg	1.289
r_mcbond_it	0.792
r_mcbond_other	0.757
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	910
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing