3TLP | pdb_00003tlp

Crystal structure of the fourth 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	3HMF	PDB entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY
experimental model	PDB	2OO1	PDB entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY
experimental model	PDB	3DAI	PDB entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY
experimental model	PDB	3HMH	PDB entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY
experimental model	PDB	2OSS	PDB entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY
experimental model	PDB	2OUO	PDB entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY
experimental model	PDB	3D7C	PDB entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY
experimental model	PDB	3DWY	PDB entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	25% PEG_MME_2000, 0.015M NiCl, 0.1M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.431	α = 90
b = 60.22	β = 90
c = 109.907	γ = 90

Symmetry
Space Group	P 21 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	PIXEL	PSI PILATUS 6M		2011-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.000	Diamond	I03

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	2.13	19.75	99.4	0.062	0.062	14.3	4.4	18984	18871			44.7

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	2.13	2.25	99.8		0.88	0.88	0.9	4.3	2738

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 entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY	2.13	19.75	19003	18831	973	99.09	0.2037	0.2037	0.2014	0.2	0.2486	0.24	RANDOM	50.8461

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]
0.51			0.04		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.493
r_dihedral_angle_4_deg	20.708
r_dihedral_angle_3_deg	15.792
r_dihedral_angle_1_deg	5.315
r_angle_refined_deg	1.324
r_angle_other_deg	1.173
r_chiral_restr	0.08
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1889
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	4

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
GDA	data collection
XDS	data reduction