5IGL

Crystal structure of the second bromodomain of human TAF1L in complex with bromosporine (BSP)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	63%(v/v) MPD, 0.1M MMT pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.172	α = 90
b = 89.177	β = 90
c = 117.892	γ = 90

Symmetry
Space Group	I 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	DECTRIS PILATUS 6M		2013-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

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	2.1	44.46	99.6	0.036	0.022	16.6	3.6		13934			38.5

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	2.21	99.7		0.369	2.7	3.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2GRC, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY	2.1	44.46	13238	695	99.42	0.21484	0.2112	0.29418	RANDOM	67.071

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]
7.67			-1.83		-5.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.641
r_scangle_other	21.548
r_long_range_B_other	21.161
r_long_range_B_refined	21.143
r_dihedral_angle_3_deg	19.846
r_scbond_it	19.054
r_scbond_other	19.038
r_mcangle_it	16.475
r_mcangle_other	16.47
r_dihedral_angle_4_deg	16.344
r_mcbond_other	13.701
r_mcbond_it	13.686
r_dihedral_angle_1_deg	6.519
r_angle_refined_deg	2.337
r_angle_other_deg	1.299
r_chiral_restr	0.153
r_bond_refined_d	0.025
r_gen_planes_refined	0.013
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1095
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing