9FBX | pdb_00009fbx

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 5-(1-benzyl-4-chloro-1H-imidazol-2-yl)-1,3-dimethylpyridin-2(1H)-one

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		in house

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.755	α = 90
b = 52.427	β = 90
c = 31.92	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		2015-06-03	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)	CC (Half)	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	1.6	29.2	94.1	0.013	0.998	52.8	2.8		15367

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.69	75.5		0.034	0.984	21.7	1.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.602	29.182	15296	730	92.979	0.151	0.1501	0.16	0.1751	0.18	14.39

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]
-0.118			-0.037		0.155

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.064
r_dihedral_angle_3_deg	13.125
r_lrange_it	5.475
r_lrange_other	5.473
r_dihedral_angle_1_deg	4.756
r_dihedral_angle_2_deg	4.411
r_scangle_it	2.372
r_scangle_other	2.37
r_mcangle_other	1.885
r_mcangle_it	1.878
r_scbond_it	1.391
r_scbond_other	1.39
r_mcbond_it	1.064
r_mcbond_other	1.034
r_angle_refined_deg	0.991
r_angle_other_deg	0.371
r_nbd_refined	0.211
r_nbtor_refined	0.186
r_symmetry_nbd_other	0.179
r_nbd_other	0.122
r_xyhbond_nbd_refined	0.097
r_symmetry_nbd_refined	0.076
r_symmetry_nbtor_other	0.073
r_symmetry_xyhbond_nbd_refined	0.071
r_chiral_restr	0.055
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	926
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	54

Software

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