3UV5 | pdb_00003uv5

Crystal Structure of the tandem bromodomains of human Transcription initiation factor TFIID subunit 1 (TAF1)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HMH	Ensemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental model	PDB	2GRC	Ensemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental model	PDB	2OO1	Ensemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental model	PDB	2OSS	Ensemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental model	PDB	2OUO	Ensemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental model	PDB	3DAI	Ensemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental model	PDB	3D7C	Ensemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental model	PDB	3DWY	Ensemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental model	PDB	3G0L	Ensemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental model	PDB	3GG3	Ensemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	293	0.1M Tris-HCl, 1.1M (NH4)2SO4, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.1	70.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.76	α = 90
b = 199.99	β = 90
c = 88.02	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	ADSC QUANTUM 315		2010-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97	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	2.03	34.482	99.2	0.092	0.092	11.5	6.5	33444	33176			35.7

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	2.03	2.14	95.1		0.741	0.741	1	4.4	4587

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	Ensemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3	2.03	34.48	33474	33153	1678	99.04	0.192	0.192	0.1901	0.19	0.2297	0.23	RANDOM	40.9279

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]
-0.38			1.3		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.086
r_dihedral_angle_4_deg	23.119
r_dihedral_angle_3_deg	14.833
r_dihedral_angle_1_deg	5.382
r_angle_refined_deg	1.649
r_angle_other_deg	0.988
r_chiral_restr	0.096
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.086
r_dihedral_angle_4_deg	23.119
r_dihedral_angle_3_deg	14.833
r_dihedral_angle_1_deg	5.382
r_angle_refined_deg	1.649
r_angle_other_deg	0.988
r_chiral_restr	0.096
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2059
Nucleic Acid Atoms
Solvent Atoms	219
Heterogen Atoms	8

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.