2DWW

Crystal structure of Bromodomain-containing protein 4


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8293NACL, PH 8.0, VAPOR DIFFUSION, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.891α = 90
b = 57.779β = 90
c = 33.588γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC QUANTUM 42005-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A1.0Photon FactoryBL-6A

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
11.775093.90.0436.813760-3
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)
1.771.8399.90.1126.4

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 REPLACEMENTTHROUGHOUTBRD2-BD21.8201236465293.60.1890.1860.245RANDOM26.57
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]
-1.921.70.22
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it7.234
r_scbond_it5.772
r_dihedral_angle_1_deg5.277
r_mcangle_it3.889
r_mcbond_it2.963
r_angle_refined_deg1.235
r_symmetry_vdw_refined0.252
r_nbd_refined0.225
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.156
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it7.234
r_scbond_it5.772
r_dihedral_angle_1_deg5.277
r_mcangle_it3.889
r_mcbond_it2.963
r_angle_refined_deg1.235
r_symmetry_vdw_refined0.252
r_nbd_refined0.225
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.156
r_chiral_restr0.092
r_bond_refined_d0.019
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms925
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms2

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling