3G0L

Crystal Structure of Human Bromodomain Adjacent to Zinc finger domain 2B (BAZ2B)


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 DROP62770.1M MMT pH 6.0, 30% PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
4.270.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.434α = 90
b = 96.314β = 90
c = 57.641γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5

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
12.0323.6296.40.0790.07912.53.7151051456131
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)
12.032.1494.40.6060.60623.72066

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, 3DAI2.0322.22152011454772895.70.1790.1790.1780.211RANDOM17.301
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]
2.01-0.99-1.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.219
r_dihedral_angle_4_deg17.664
r_dihedral_angle_3_deg11.263
r_scangle_it8.573
r_scbond_it7.685
r_dihedral_angle_1_deg5.159
r_mcangle_it4.354
r_mcbond_it3.128
r_angle_refined_deg1.35
r_mcbond_other1.051
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.219
r_dihedral_angle_4_deg17.664
r_dihedral_angle_3_deg11.263
r_scangle_it8.573
r_scbond_it7.685
r_dihedral_angle_1_deg5.159
r_mcangle_it4.354
r_mcbond_it3.128
r_angle_refined_deg1.35
r_mcbond_other1.051
r_angle_other_deg0.899
r_chiral_restr0.08
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms927
Nucleic Acid Atoms
Solvent Atoms134
Heterogen Atoms4

Software

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