6TPZ | pdb_00006tpz

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 5-(1-(1,3-dimethoxypropan-2-yl)-5-morpholino-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
other		not published

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	of 0.1 PCTP pH 8.0, 25% v/v PEG1500

Crystal Properties
Matthews coefficient	Solvent content
1.89	34.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.493	α = 90
b = 49.533	β = 90
c = 58.213	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 6M		2015-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97949	Diamond	I03

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	1.299	49.53	99.7	0.999	30.5	5.9		28760

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	1.299	1.37	98.6		0.987	11.2

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	not published	1.299	37.725	28705	1407	99.591	0.193	0.1915	0.2	0.2176	0.22	17.491

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]
-0.211			0.481		-0.271

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.96
r_dihedral_angle_4_deg	15.024
r_dihedral_angle_3_deg	12.372
r_lrange_it	5.362
r_lrange_other	5.36
r_dihedral_angle_1_deg	5.123
r_scangle_it	2.296
r_scangle_other	2.294
r_mcangle_it	1.803
r_mcangle_other	1.802
r_scbond_it	1.362
r_scbond_other	1.361
r_angle_other_deg	1.188
r_angle_refined_deg	1.144
r_mcbond_it	1.048
r_mcbond_other	1.042
r_nbd_other	0.201
r_nbd_refined	0.191
r_nbtor_refined	0.169
r_symmetry_nbd_other	0.16
r_symmetry_nbd_refined	0.121
r_xyhbond_nbd_refined	0.117
r_symmetry_xyhbond_nbd_refined	0.099
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.057
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	1043
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	39

Software

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