6ZB0

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1-benzyl-N-methyl-2-oxo-1,2-dihydropyridine-3-carboxamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		in house structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	30% PEG 300, 0.1M MES buffer pH6.5

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.106	α = 90
b = 52.758	β = 90
c = 32.318	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	RIGAKU SATURN A200		2014-08-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.54178

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	1.61	36.05	95.5	0.019	31.9	2.7		15692

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	1.61	1.7	81.8		0.065	11.2	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	in house structure	1.613	29.491	15647	787	94.721	0.141	0.1393	0.1775	14.632

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]
0.012			0.017		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.653
r_dihedral_angle_4_deg	23.709
r_dihedral_angle_3_deg	12.475
r_lrange_it	5.912
r_lrange_other	5.91
r_dihedral_angle_1_deg	5.334
r_scangle_it	2.206
r_scangle_other	2.204
r_mcangle_other	1.509
r_mcangle_it	1.506
r_angle_other_deg	1.409
r_scbond_other	1.345
r_scbond_it	1.343
r_angle_refined_deg	1.325
r_mcbond_it	0.906
r_mcbond_other	0.835
r_nbd_refined	0.214
r_nbtor_refined	0.178
r_symmetry_nbd_other	0.174
r_nbd_other	0.139
r_symmetry_nbd_refined	0.124
r_xyhbond_nbd_refined	0.118
r_symmetry_xyhbond_nbd_refined	0.114
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.079
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	941
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	34

Software

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