2DVR | pdb_00002dvr

Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with acetylated histone H4 peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		BD1 NATIVE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, CO-CRYSTALLIZAATION	6.5	298	PEGMME 5K, AS, pH 6.50, VAPOR DIFFUSION, CO-CRYSTALLIZAATION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.3	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.533	α = 90
b = 55.238	β = 93.92
c = 67.735	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	120	CCD	ADSC		2004-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2		SPring-8	BL44B2

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	2.04	50	98.4	0.062		3.6		26362		-3

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)
	2.04	2.11	88.8		0.331		3

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	BD1 NATIVE	2.3	20	17759	965	99.8	0.182	0.18	0.243	RANDOM	34.63

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]
0.67		-1.3	-0.35		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.851
r_scangle_it	4.467
r_scbond_it	2.982
r_mcangle_it	1.736
r_angle_refined_deg	1.691
r_mcbond_it	0.918
r_symmetry_hbond_refined	0.414
r_symmetry_vdw_refined	0.27
r_nbd_refined	0.251
r_xyhbond_nbd_refined	0.181
r_chiral_restr	0.116
r_bond_refined_d	0.022
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2887
Nucleic Acid Atoms
Solvent Atoms	250
Heterogen Atoms

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling