6TPX | pdb_00006tpx

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 1-((1-acetylpiperidin-4-yl)methyl)-2-(4-hydroxy-3,5-dimethylphenyl)-N-methyl-1H-benzo[d]imidazole-5-carboxamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		non published structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	20% PEG6000, 0.2M NH4Cl, 0.1M tris pH8

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.868	α = 90
b = 48.684	β = 90
c = 57.629	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 PILATUS3 S 6M		2011-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.976	ESRF	ID29

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	1.48	57.63	95.6	0.025	28	5.7		19018

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	1.48	1.53			0.128	7.2	3.5

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	non published structure	1.48	37.218	18971	978	95.471	0.156	0.1552	0.16	0.1814	0.19	19.439

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]
1.047			0.195		-1.242

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.14
r_dihedral_angle_3_deg	12.753
r_dihedral_angle_4_deg	12.108
r_dihedral_angle_1_deg	5.76
r_lrange_it	5.166
r_lrange_other	5.164
r_scangle_it	2.319
r_scangle_other	2.318
r_mcangle_it	1.618
r_mcangle_other	1.618
r_scbond_it	1.398
r_scbond_other	1.397
r_angle_other_deg	1.283
r_angle_refined_deg	1.222
r_mcbond_it	0.949
r_mcbond_other	0.947
r_nbd_refined	0.203
r_nbd_other	0.189
r_nbtor_refined	0.175
r_symmetry_nbd_other	0.16
r_symmetry_nbd_refined	0.124
r_xyhbond_nbd_refined	0.106
r_symmetry_xyhbond_nbd_refined	0.106
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.065
r_gen_planes_refined	0.006
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	214
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction