6Z8P | pdb_00006z8p

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH GSK973

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		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 = 71.877	α = 90
b = 52.473	β = 90
c = 32.07	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		2016-10-25	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	1.55	42.38	89.2	0.024	31.6	3.4		16200

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	1.55	1.64	52.5		0.186	4.7	2

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	FOURIER SYNTHESIS	FREE R-VALUE	in house model	1.55	42.38	16128	769	88.223	0.166	0.1648	0.17	0.1947	0.2	19.837

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]
-0.008			-0.004		0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.594
r_dihedral_angle_4_deg	18.771
r_dihedral_angle_3_deg	11.856
r_lrange_it	5.921
r_lrange_other	5.919
r_dihedral_angle_1_deg	4.646
r_scangle_it	2.462
r_scangle_other	2.461
r_mcangle_other	2.04
r_mcangle_it	2.037
r_scbond_it	1.453
r_scbond_other	1.451
r_angle_other_deg	1.245
r_mcbond_it	1.169
r_angle_refined_deg	1.163
r_mcbond_other	1.145
r_nbd_refined	0.194
r_nbtor_refined	0.167
r_symmetry_nbd_other	0.166
r_nbd_other	0.143
r_symmetry_nbd_refined	0.136
r_xyhbond_nbd_refined	0.095
r_symmetry_xyhbond_nbd_refined	0.091
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.06
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_symmetry_xyhbond_nbd_other	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	926
Nucleic Acid Atoms
Solvent Atoms	228
Heterogen Atoms	56

Software

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