8PX8 | pdb_00008px8

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH (S)-5-(1-((1-acetylpiperidin-3-yl)methyl)-5-bromo-1H-benzo[d]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	6.5	293	30% PEG 300, 0.1M MES buffer pH6.5

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.825	α = 90
b = 52.573	β = 90
c = 31.975	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		2014-12-03	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)	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	71.82	96.6	0.018	40.9	3.3		15930

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	1.6	1.69	81		0.068	12.2	2

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	FOURIER SYNTHESIS	FREE R-VALUE	1.603	42.423	15868	766	96.141	0.145	0.1436	0.16	0.1713	0.19	14.874

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]
0.818			-0.794		-0.024

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.099
r_dihedral_angle_3_deg	13.176
r_lrange_it	6.491
r_lrange_other	6.489
r_dihedral_angle_1_deg	5.092
r_dihedral_angle_2_deg	4.629
r_scangle_it	3.091
r_scangle_other	3.089
r_scbond_it	1.918
r_scbond_other	1.916
r_mcangle_other	1.501
r_mcangle_it	1.497
r_angle_refined_deg	1.085
r_mcbond_it	0.951
r_mcbond_other	0.904
r_angle_other_deg	0.411
r_nbd_refined	0.23
r_nbtor_refined	0.189
r_symmetry_nbd_other	0.173
r_symmetry_nbd_refined	0.138
r_xyhbond_nbd_refined	0.133
r_nbd_other	0.131
r_symmetry_xyhbond_nbd_refined	0.129
r_symmetry_nbtor_other	0.069
r_chiral_restr	0.061
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	910
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	45

Software

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