5IBN

Ultra high resolution crystal structure of the apo- form of second bromodomain of BRD2.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E3K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.330030% PEG MME 2000, 20% glycerol, 50mM NaCl, 50mM Tris pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.346.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.08α = 90
b = 52.46β = 90
c = 71.37γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDGrazing angle 2.8 mrad2015-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.7293ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
10.9442.2499.70.0899.5878817
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)
10.940.991002.26817.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT2e3k0.942074948388999.630.129210.128410.1451RANDOM13.809
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]
0.06-0.250.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.589
r_sphericity_free29.445
r_dihedral_angle_4_deg22.753
r_dihedral_angle_3_deg12.101
r_sphericity_bonded7.949
r_dihedral_angle_1_deg4.405
r_rigid_bond_restr2.803
r_angle_refined_deg1.614
r_angle_other_deg0.888
r_chiral_restr0.099
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.589
r_sphericity_free29.445
r_dihedral_angle_4_deg22.753
r_dihedral_angle_3_deg12.101
r_sphericity_bonded7.949
r_dihedral_angle_1_deg4.405
r_rigid_bond_restr2.803
r_angle_refined_deg1.614
r_angle_other_deg0.888
r_chiral_restr0.099
r_bond_refined_d0.013
r_gen_planes_refined0.01
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms916
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Phaser_MRphasing