7P6W | pdb_00007p6w

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH compound 3bg

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%w/v PEG 4K, 0.2M Na Acet, 0.1M TRIS pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.351	α = 90
b = 52.103	β = 90
c = 57.176	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2018-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

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	1.31	34.02	98.6	0.035	0.989	17.9	6.1		30602

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	1.31	1.34	97.2		0.996	0.65		5.2

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	MOLECULAR REPLACEMENT	FREE R-VALUE	in house model	1.31	34	30543	1562	98.193	0.197	0.1954	0.2	0.2205	0.23	25.147

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]
0.714			-0.278		-0.436

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.686
r_dihedral_angle_4_deg	14.401
r_dihedral_angle_3_deg	13.078
r_lrange_it	5.704
r_lrange_other	5.702
r_dihedral_angle_1_deg	5.444
r_scangle_it	3.206
r_scangle_other	3.204
r_mcangle_it	2.297
r_mcangle_other	2.297
r_scbond_it	1.967
r_scbond_other	1.966
r_mcbond_it	1.423
r_mcbond_other	1.422
r_angle_other_deg	1.212
r_angle_refined_deg	1.18
r_nbd_refined	0.194
r_symmetry_nbd_refined	0.181
r_nbd_other	0.173
r_nbtor_refined	0.171
r_symmetry_nbd_other	0.168
r_symmetry_xyhbond_nbd_refined	0.163
r_xyhbond_nbd_refined	0.111
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.056
r_gen_planes_refined	0.007
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1061
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	48

Software

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