3G0J | pdb_00003g0j

Crystal Structure of the fifth Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DWY	ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC
experimental model	PDB	3DAI	ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC
experimental model	PDB	3D7C	ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC
experimental model	PDB	2OUO	ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC
experimental model	PDB	2OSS	ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC
experimental model	PDB	2OO1	ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC
experimental model	PDB	2NXB	ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC
experimental model	PDB	2GRC	ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.2M Na_nitrate, 25% w/v PEG 3350, 5% v/v ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.57	α = 90
b = 57.37	β = 90
c = 137.3	γ = 90

Symmetry
Space Group	P 2 21 21

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		2008-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5

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	1.78	30.831	98.9	0.079	0.079	18.2	8.8	28619	28304			22.8

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	1.78	1.88	100		0.703	0.703	2.6	9	4085

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 (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	ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC	1.78	29.45	28246	1428	98.84	0.193	0.193	0.19	0.2	0.237	0.25	RANDOM	15.392

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]
0.45			-0.29		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.468
r_dihedral_angle_3_deg	14.478
r_dihedral_angle_4_deg	13.52
r_scangle_it	6.667
r_scbond_it	5.21
r_dihedral_angle_1_deg	5.187
r_mcangle_it	3.557
r_mcbond_it	2.808
r_angle_refined_deg	1.373
r_mcbond_other	1.266
r_angle_other_deg	0.926
r_chiral_restr	0.083
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1870
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms	20

Software

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