8PXA | pdb_00008pxa

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH (S)-5-(1-((1-(1-isopropylpiperidine-4-carbonyl)piperidin-3-yl)methyl)-1H-benzo[d]imidazol-2-yl)-1,3-dimethylpyridin-2(1H)-one

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		in house structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	0.1M Tris pH8.5, 12% w/v PEG4K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.845	α = 90
b = 47.236	β = 90
c = 58.974	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		2019-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979507	Diamond	I04

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	1.3	58.97	98.5	0.06	0.999	13.8	5.8		31016

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	1.3	1.37	90.4		0.475	0.751	1.9	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.3	32.544	30959	1588	98.304	0.199	0.1984	0.21	0.2175	0.23	17.014

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]
-0.18			0.009		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.453
r_dihedral_angle_3_deg	10.913
r_dihedral_angle_4_deg	8.102
r_dihedral_angle_1_deg	5.887
r_lrange_it	4.634
r_lrange_other	4.174
r_scangle_it	2.058
r_scangle_other	2.057
r_mcangle_it	1.398
r_mcangle_other	1.393
r_scbond_it	1.276
r_scbond_other	1.275
r_angle_other_deg	1.203
r_angle_refined_deg	1.193
r_mcbond_it	0.855
r_mcbond_other	0.849
r_nbd_refined	0.189
r_nbtor_refined	0.172
r_symmetry_nbd_other	0.165
r_nbd_other	0.152
r_xyhbond_nbd_refined	0.128
r_symmetry_xyhbond_nbd_refined	0.12
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.062
r_symmetry_nbd_refined	0.058
r_gen_planes_refined	0.004
r_bond_refined_d	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	1046
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	36

Software

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