3UV2

Crystal structure of the bromodomain of human nucleosome-remodeling factor subunit BPTF


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NXBEnsemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental modelPDB 2OO1Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental modelPDB 2OSSEnsemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental modelPDB 2OUOEnsemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental modelPDB 2RFJEnsemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental modelPDB 3DAIEnsemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.10M Na/KPO4, 20.0% PEG 3350, 10.0% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3146.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 27.141α = 90
b = 66.809β = 106.16
c = 39.259γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-07-03MSINGLE 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
11.582593.30.050.0515.93.7184601722319.6
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)
11.581.6779.50.5180.5181.53.42102

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 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI1.5825184571722288193.310.16470.16470.16230.209RANDOM18.3808
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]
0.230.59-0.510.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.25
r_dihedral_angle_4_deg17.842
r_dihedral_angle_3_deg12.553
r_dihedral_angle_1_deg4.967
r_angle_refined_deg1.671
r_angle_other_deg0.957
r_chiral_restr0.098
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.25
r_dihedral_angle_4_deg17.842
r_dihedral_angle_3_deg12.553
r_dihedral_angle_1_deg4.967
r_angle_refined_deg1.671
r_angle_other_deg0.957
r_chiral_restr0.098
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms983
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms10

Software

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