3P1E | pdb_00003p1e

Crystal structure of the bromodomain of human CREBBP in complex with dimethyl sulfoxide (DMSO)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.2M KSCN 25% PEG3350 5% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.85	α = 90
b = 121.85	β = 90
c = 40.55	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2010-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.542

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.8	28.435	99.9	0.095	0.095	4.8	2.3	20837	20816			23.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.9	99.9		0.456	0.456	1.1	2.2	3057

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	3DWY	1.8	28.435	20832	20807	1050	99.88	0.1823	0.1823	0.1795	0.18	0.2357	0.23	RANDOM	26.326

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]
-0.31	-0.16		-0.31		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.29
r_dihedral_angle_4_deg	21.518
r_dihedral_angle_3_deg	13.9
r_scangle_it	8.67
r_scbond_it	6.577
r_dihedral_angle_1_deg	5.513
r_mcangle_it	4.45
r_mcbond_it	3.272
r_angle_refined_deg	1.45
r_mcbond_other	1.104

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.29
r_dihedral_angle_4_deg	21.518
r_dihedral_angle_3_deg	13.9
r_scangle_it	8.67
r_scbond_it	6.577
r_dihedral_angle_1_deg	5.513
r_mcangle_it	4.45
r_mcbond_it	3.272
r_angle_refined_deg	1.45
r_mcbond_other	1.104
r_angle_other_deg	0.97
r_chiral_restr	0.089
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1846
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	12

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

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.