5IGL

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GRC2GRC, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 2NXB2GRC, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 2OO12GRC, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 2OSS2GRC, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 2OUO2GRC, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 2RFJ2GRC, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 3DAI2GRC, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 3D7C2GRC, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 3DWY2GRC, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527763%(v/v) MPD, 0.1M MMT pH 7.5
Crystal Properties
Matthews coefficientSolvent content
3.2261.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.172α = 90
b = 89.177β = 90
c = 117.892γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

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
12.144.4699.60.0360.02216.63.61393438.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2199.70.3692.73.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2GRC, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY2.144.461323869599.420.214840.21120.29418RANDOM67.071
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.641
r_scangle_other21.548
r_long_range_B_other21.161
r_long_range_B_refined21.143
r_dihedral_angle_3_deg19.846
r_scbond_it19.054
r_scbond_other19.038
r_mcangle_it16.475
r_mcangle_other16.47
r_dihedral_angle_4_deg16.344
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.641
r_scangle_other21.548
r_long_range_B_other21.161
r_long_range_B_refined21.143
r_dihedral_angle_3_deg19.846
r_scbond_it19.054
r_scbond_other19.038
r_mcangle_it16.475
r_mcangle_other16.47
r_dihedral_angle_4_deg16.344
r_mcbond_other13.701
r_mcbond_it13.686
r_dihedral_angle_1_deg6.519
r_angle_refined_deg2.337
r_angle_other_deg1.299
r_chiral_restr0.153
r_bond_refined_d0.025
r_gen_planes_refined0.013
r_bond_other_d0.003
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms1095
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing