8B5G | pdb_00008b5g

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 7,8-dimethoxy-3-methyl-1,3-dihydro-2H-benzo[d]azepin-2-one

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.906	α = 90
b = 52.421	β = 90
c = 32.086	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		2014-11-21	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	1.619	71.39	96.3	0.013	52.1	2.5		15360

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	1.619	1.71	85		0.031	22.2	1.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	In house	1.619	21.808	15248	758	94.938	0.15	0.1483	0.15	0.1827	0.19	13.384

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]
0.094			-0.051		-0.043

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.061
r_dihedral_angle_4_deg	18.736
r_dihedral_angle_3_deg	11.322
r_lrange_it	5.005
r_lrange_other	5.003
r_dihedral_angle_1_deg	4.939
r_scangle_it	1.663
r_scangle_other	1.662
r_angle_other_deg	1.35
r_angle_refined_deg	1.23
r_mcangle_other	1.213
r_mcangle_it	1.211
r_scbond_it	0.985
r_scbond_other	0.985
r_mcbond_it	0.694
r_mcbond_other	0.668
r_nbd_refined	0.206
r_nbtor_refined	0.173
r_symmetry_nbd_other	0.166
r_symmetry_nbd_refined	0.147
r_nbd_other	0.13
r_xyhbond_nbd_refined	0.107
r_symmetry_xyhbond_nbd_refined	0.095
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.068
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	915
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	37

Software

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