4NR9

Crystal Structure of the bromodomain of human BAZ2B in complex with acetylated lysine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G0Lpdb entry 3G0L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.7277.1530% low MW PEG Smears, 0.1M MES pH 6.7, 15%(v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
4.2370.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.439α = 90
b = 96.754β = 90
c = 57.754γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2011-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.9819.6799.90.08410.951643716407
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)
11.982.091000.7162.15

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 3G0L1.9819.5164071557583099.690.192960.19090.23335RANDOM41.368
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]
2.67-0.68-1.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.473
r_dihedral_angle_3_deg14.086
r_dihedral_angle_4_deg13.661
r_long_range_B_refined7.676
r_long_range_B_other7.673
r_dihedral_angle_1_deg5.701
r_scangle_other3.879
r_mcangle_it2.771
r_mcangle_other2.76
r_scbond_other2.544
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.473
r_dihedral_angle_3_deg14.086
r_dihedral_angle_4_deg13.661
r_long_range_B_refined7.676
r_long_range_B_other7.673
r_dihedral_angle_1_deg5.701
r_scangle_other3.879
r_mcangle_it2.771
r_mcangle_other2.76
r_scbond_other2.544
r_scbond_it2.524
r_mcbond_it1.961
r_mcbond_other1.937
r_angle_refined_deg1.633
r_angle_other_deg0.816
r_chiral_restr0.084
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms941
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms29

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling