5I86 | pdb_00005i86

Crystal structure of the bromodomain of human CREBBP bound to the benzodiazepinone G02778174

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	0.2 M potassium thiocyanate, 0.1 M Bis-Tris, pH 5.5, 5% v/v ethylene glycol, 23% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.993	α = 96.77
b = 42.002	β = 109.7
c = 49.8	γ = 99.39

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX-300		2012-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9795	CLSI	08ID-1

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	1.05	50	92.7	0.032	13	2.2		108956

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	1.05	1.09	87.8		0.376		2.1

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	PDB entry 3DWY	1.05	40.71	103515	5440	92.61	0.14	0.1389	0.1485	0.1614	0.1695	RANDOM	15.536

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]
0.14	0.22	-0.23	0.37	0.27	-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.593
r_sphericity_free	23.645
r_dihedral_angle_4_deg	18.922
r_dihedral_angle_3_deg	12.259
r_sphericity_bonded	11.453
r_rigid_bond_restr	6.583
r_dihedral_angle_1_deg	5.752
r_mcangle_it	1.585
r_angle_refined_deg	1.583
r_mcbond_it	1.475
r_mcbond_other	1.387
r_angle_other_deg	0.762
r_chiral_restr	0.097
r_gen_planes_refined	0.017
r_bond_refined_d	0.01
r_gen_planes_other	0.003
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1933
Nucleic Acid Atoms
Solvent Atoms	385
Heterogen Atoms	57

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing