4NR6 | pdb_00004nr6

Crystal structure of the bromodomain of human CREBBP in complex with an oxazepin ligand

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	6	277	0.10M MgCl2, 0.1M MES pH 6.0, 20.0% PEG 6K, 10.0% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.24	44.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.71	α = 90
b = 35.14	β = 93
c = 40.4	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	ADSC QUANTUM 315r		2012-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	1.0121	Diamond	I04

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	1.66	30.79	99	0.063	0.063	10.7	3.4	15041	14891			21.4

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	1.66	1.75	97.9		0.478	0.478	1.6	3.1	2113

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	PDB entry 3DWY	1.66	30.79	15062	14889	749	98.85	0.1809	0.1809	0.1784	0.18	0.2305	0.25	RANDOM	29.1493

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]
-1.27		-0.52	2.6		-1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.307
r_dihedral_angle_4_deg	21.922
r_dihedral_angle_3_deg	16.329
r_dihedral_angle_1_deg	5.93
r_angle_refined_deg	1.698
r_angle_other_deg	0.956
r_chiral_restr	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.307
r_dihedral_angle_4_deg	21.922
r_dihedral_angle_3_deg	16.329
r_dihedral_angle_1_deg	5.93
r_angle_refined_deg	1.698
r_angle_other_deg	0.956
r_chiral_restr	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	965
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	34

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	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.