3UVD

Crystal Structure of the bromodomain of human Transcription activator BRG1 (SMARCA4) in complex with N-Methyl-2-pyrrolidone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GRCEnsemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental modelPDB 2OSSEnsemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental modelPDB 2OUOEnsemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental modelPDB 2OO1Ensemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental modelPDB 3DAIEnsemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental modelPDB 3D7CEnsemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental modelPDB 3DWYEnsemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental modelPDB 3G0LEnsemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental modelPDB 3G0JEnsemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental modelPDB 3GG3Ensemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.527728% MMW PEG smear 0.1M Tris.HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0840.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.2α = 90
b = 29.89β = 90.45
c = 67.06γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2010-07-13MSINGLE 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
11.8529.891000.0670.067103.5104881048835.1
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)
11.851.951000.5440.5441.43.41502

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 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG31.8529.89104821047950299.970.20270.20270.19960.2624RANDOM46.1641
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]
-1.67-0.822.13-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.184
r_dihedral_angle_4_deg18.259
r_dihedral_angle_3_deg17.639
r_dihedral_angle_1_deg5.846
r_angle_refined_deg1.722
r_angle_other_deg1.035
r_chiral_restr0.104
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.184
r_dihedral_angle_4_deg18.259
r_dihedral_angle_3_deg17.639
r_dihedral_angle_1_deg5.846
r_angle_refined_deg1.722
r_angle_other_deg1.035
r_chiral_restr0.104
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms990
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms7

Software

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