2WP1 | pdb_00002wp1

Structure of Brdt bromodomain 2 bound to an acetylated histone H3 peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E6I	PDB ENTRY 1E6I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5		BRDT BD2 PROTEIN AT 25 MG/ML WAS MIXED WITH H3-ACK18 PEPTIDE IN A 1:5 MOLAR RATIO. CRYSTALLIZATION WAS BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 2.0 M AMMONIUM SULFATE, 2% PEG 400, 0.1 M HEPES PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
3.23	62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.3	α = 90
b = 101.3	β = 90
c = 79.35	γ = 90

Symmetry
Space Group	P 41 21 2

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 CCD		2007-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	2.1	40	91.2	0.11	7	7.7		22542			60.7

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	2.1	2.2	93.9		0.61	2.9	8

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 1E6I	2.1	40	22542	1143	91.2	0.234	0.234	0.22	0.255	0.2	RANDOM	72.1

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]
-0.052			-0.052		0.104

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.4
c_angle_deg	1.20706
c_improper_angle_d	0.96
c_bond_d	0.007812
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2036
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing