6YQZ | pdb_00006yqz

N-terminal domain of BRD4 with biphenyl-methyamino-dimethylpyridazinone

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	20%w/v PEG 3350, 0.2M sodium sulphate,0.1M bis-tris-propane (pH 6.5)

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.94	α = 90
b = 44.37	β = 90
c = 78.05	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 2M		2012-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97625	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.39	39.03	98.5	0.083	0.094	0.043	9	4.1		26727

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.39	1.47	95.2		0.513	0.513	0.619	0.338	1.5	2.9

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	In house structure	1.39	39.03	25379	1348	98.17	0.1732	0.1717	0.1735	0.2037	0.2039	RANDOM	18.245

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]
1.52			-0.44		-1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.96
r_dihedral_angle_3_deg	12.568
r_dihedral_angle_4_deg	10.168
r_dihedral_angle_1_deg	5.547
r_angle_other_deg	1.27
r_angle_refined_deg	1.194
r_chiral_restr	0.062
r_gen_planes_refined	0.005
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	1062
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	27

Software

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