5I89 | pdb_00005i89

Crystal structure of the bromodomain of human CREBBP bound to the benzodiazepinone G02857790

X-RAY DIFFRACTION

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 calcium acetate hydrate, and 20% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.283	α = 90
b = 34.321	β = 106.82
c = 40.005	γ = 90

Symmetry
Space Group	C 1 2 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	MARMOSAIC 225 mm CCD		2015-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.9786	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.07	50	99	0.069	0.083	0.045	11.6	3.5		53632

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	1.07	1.11	97.3		0.207		3.4

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	1.07	45.13	50979	2653	98.94	0.1176	0.1165	0.12	0.1371	0.14	RANDOM	13.397

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]
-0.09		-0.09	0.26		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.246
r_sphericity_free	34.5
r_sphericity_bonded	14.702
r_dihedral_angle_3_deg	11.977
r_dihedral_angle_4_deg	10.181
r_rigid_bond_restr	6.971
r_dihedral_angle_1_deg	6.335
r_mcangle_it	4.983
r_mcbond_it	3.939
r_mcbond_other	3.935

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.246
r_sphericity_free	34.5
r_sphericity_bonded	14.702
r_dihedral_angle_3_deg	11.977
r_dihedral_angle_4_deg	10.181
r_rigid_bond_restr	6.971
r_dihedral_angle_1_deg	6.335
r_mcangle_it	4.983
r_mcbond_it	3.939
r_mcbond_other	3.935
r_angle_refined_deg	1.38
r_angle_other_deg	0.726
r_chiral_restr	0.076
r_gen_planes_refined	0.018
r_bond_refined_d	0.009
r_gen_planes_other	0.005
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	967
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	31

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.