3UV4

Crystal Structure of the second bromodomain of human Transcription initiation factor TFIID subunit 1 (TAF1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HMHEnsemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental modelPDB 2GRCEnsemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental modelPDB 2OO1Ensemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental modelPDB 2OSSEnsemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental modelPDB 2OUOEnsemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental modelPDB 3DAIEnsemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental modelPDB 3D7CEnsemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental modelPDB 3DWYEnsemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental modelPDB 3G0LEnsemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3
experimental modelPDB 3GG3Ensemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.056M NaH2PO4 1.344M K2HPO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7955.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.45α = 90
b = 57.8β = 90
c = 123.57γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2009-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.52

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8928.9699.20.0740.07414.44.7336863341728.4
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)RedundancyNumber Unique Reflections (All)
11.891.9997.80.7630.76314.74734

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTEnsemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG31.8928.96336663323898.730.19240.19240.1906RANDOM28.982
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]
0.680.12-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.662
r_dihedral_angle_4_deg21.594
r_dihedral_angle_3_deg12.505
r_scangle_it8.363
r_scbond_it6.803
r_dihedral_angle_1_deg4.889
r_mcangle_it4.413
r_mcbond_it3.157
r_angle_refined_deg1.356
r_mcbond_other1.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.662
r_dihedral_angle_4_deg21.594
r_dihedral_angle_3_deg12.505
r_scangle_it8.363
r_scbond_it6.803
r_dihedral_angle_1_deg4.889
r_mcangle_it4.413
r_mcbond_it3.157
r_angle_refined_deg1.356
r_mcbond_other1.09
r_angle_other_deg0.955
r_chiral_restr0.09
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2008
Nucleic Acid Atoms
Solvent Atoms305
Heterogen Atoms23

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction