4RVR

Crystal Structure of the bromodomain of human BAZ2B in complex WITH GSK2801


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5277.1528% Low Molecular-Weight PEG Smears, 0.1M MES pH 6.5 (Ligand soaking performed in low-molecular-weight PEG smears stabilizing solution) , VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
4.2771.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.72α = 90
b = 96.975β = 90
c = 58.06γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2012-03-29MSINGLE 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
11.9831.431000.06213.55166351661139.7
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)
11.982.091000.6472.152385

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUT3G0L1.9830.112166111577084199.80.189150.186860.23196RANDOM44.683
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]
1.210.08-1.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.634
r_dihedral_angle_4_deg16.825
r_dihedral_angle_3_deg13.474
r_long_range_B_refined12.494
r_long_range_B_other12.491
r_scangle_other10.503
r_scbond_it7.99
r_scbond_other7.985
r_mcangle_it7.972
r_mcangle_other7.967
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.634
r_dihedral_angle_4_deg16.825
r_dihedral_angle_3_deg13.474
r_long_range_B_refined12.494
r_long_range_B_other12.491
r_scangle_other10.503
r_scbond_it7.99
r_scbond_other7.985
r_mcangle_it7.972
r_mcangle_other7.967
r_mcbond_it6.122
r_dihedral_angle_1_deg6.063
r_mcbond_other6.051
r_angle_refined_deg1.505
r_angle_other_deg0.741
r_chiral_restr0.083
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 Atoms948
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms50

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling