5LUU

Structure of the first bromodomain of BRD4 with a pyrazolo[4,3-c]pyridin fragment


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52770.2M Na2SO4 0.1M BTProp pH 8.5 20% PEG3350 10% EtGly
Crystal Properties
Matthews coefficientSolvent content
2.1643.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.75α = 90
b = 44.21β = 90
c = 78.27γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2011-05-27MSINGLE 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 Sym I (Observed)Rrim I (All)Rpim I (All)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
11.6121.46399.40.0640.0730.03413.34.51750817508
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)
11.611.796.10.571.33.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6121.461657888599.320.17090.1690.206RANDOM14.367
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]
0.68-0.19-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.137
r_dihedral_angle_4_deg23.131
r_dihedral_angle_3_deg12.71
r_scangle_it9.009
r_scbond_it6.405
r_dihedral_angle_1_deg5.755
r_mcangle_it4.127
r_mcbond_it2.501
r_angle_refined_deg1.496
r_angle_other_deg0.953
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.137
r_dihedral_angle_4_deg23.131
r_dihedral_angle_3_deg12.71
r_scangle_it9.009
r_scbond_it6.405
r_dihedral_angle_1_deg5.755
r_mcangle_it4.127
r_mcbond_it2.501
r_angle_refined_deg1.496
r_angle_other_deg0.953
r_mcbond_other0.755
r_chiral_restr0.092
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1057
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms27

Software

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