6ZF9 | pdb_00006zf9

CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound SSR4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MXF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	20% w/v MMW PgSm, 100mM MES pH 6, 150 mM Ammonium nitrate, 5% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.36	α = 90
b = 44.13	β = 90
c = 77.79	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		2018-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.2	77.79	95.7	0.999	21.7	5.1		39219

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.22			0.961

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	3MXF	1.2	38.895	39155	1963	95.507	0.125	0.1235	0.12	0.1485	0.15	9.616

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]
-0.398			0.655		-0.256

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.473
r_dihedral_angle_3_deg	10.762
r_dihedral_angle_4_deg	10.331
r_dihedral_angle_1_deg	6.061
r_lrange_it	2.945
r_lrange_other	2.939
r_scangle_it	1.715
r_scangle_other	1.714
r_angle_refined_deg	1.61
r_angle_other_deg	1.557
r_scbond_it	1.488
r_scbond_other	1.487
r_rigid_bond_restr	1.318
r_mcangle_other	1.176
r_mcangle_it	1.172
r_mcbond_it	0.873
r_mcbond_other	0.872
r_nbd_refined	0.231
r_nbtor_refined	0.19
r_nbd_other	0.188
r_symmetry_nbd_other	0.168
r_xyhbond_nbd_refined	0.151
r_symmetry_xyhbond_nbd_refined	0.123
r_symmetry_nbd_refined	0.11
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1046
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
REFMAC	phasing