7OEP | pdb_00007oep

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 5-(1-(1,3-dimethoxypropan-2-yl)-5-morpholino-1H-benzo[d]imidazol-2-yl)-1,3-dimethylpyridin-2(1H)-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin house structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29330% PEG 300, 0.1M MES buffer pH6.5
Crystal Properties
Matthews coefficientSolvent content
2.2745.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.735α = 90
b = 53.152β = 90
c = 32.046γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002015-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.826.5898.50.0350.99220.22.911665
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.9799.40.1790.76552.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUEin house structure1.80126.51147157096.4190.1760.17340.180.2370.2417.987
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]
0.326-0.312-0.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.363
r_dihedral_angle_4_deg22.699
r_dihedral_angle_3_deg12.884
r_lrange_it5.848
r_lrange_other5.846
r_dihedral_angle_1_deg5.146
r_scangle_it2.199
r_scangle_other2.197
r_mcangle_other1.676
r_mcangle_it1.675
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.363
r_dihedral_angle_4_deg22.699
r_dihedral_angle_3_deg12.884
r_lrange_it5.848
r_lrange_other5.846
r_dihedral_angle_1_deg5.146
r_scangle_it2.199
r_scangle_other2.197
r_mcangle_other1.676
r_mcangle_it1.675
r_angle_refined_deg1.346
r_scbond_it1.317
r_scbond_other1.316
r_angle_other_deg1.255
r_mcbond_it0.96
r_mcbond_other0.956
r_symmetry_nbd_refined0.228
r_nbd_refined0.197
r_nbd_other0.192
r_symmetry_nbd_other0.175
r_symmetry_xyhbond_nbd_refined0.17
r_nbtor_refined0.169
r_xyhbond_nbd_refined0.143
r_symmetry_nbtor_other0.083
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms931
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling