8B5I | pdb_00008b5i

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 7,8-dimethoxy-1,3-dimethyl-1,3-dihydro-2H-benzo[d]azepin-2-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin hosue

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29530% PEG 300, 0.1M MES buffer pH6.5
Crystal Properties
Matthews coefficientSolvent content
2.2445.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.793α = 90
b = 52.4β = 90
c = 31.972γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray199CCDRIGAKU SATURN A2002015-02-11MSINGLE 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
11.631.99296.90.0180.99835.72.915915
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)
11.61.6983.30.0750.8019.61.8

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 DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEin hosue1.60431.9921582076196.2050.1480.14650.160.17880.1916.309
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]
-0.1120.187-0.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.201
r_dihedral_angle_4_deg20.021
r_dihedral_angle_3_deg10.615
r_lrange_it5.244
r_lrange_other5.243
r_dihedral_angle_1_deg4.667
r_scangle_it2.141
r_scangle_other2.14
r_angle_other_deg1.323
r_scbond_it1.274
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.201
r_dihedral_angle_4_deg20.021
r_dihedral_angle_3_deg10.615
r_lrange_it5.244
r_lrange_other5.243
r_dihedral_angle_1_deg4.667
r_scangle_it2.141
r_scangle_other2.14
r_angle_other_deg1.323
r_scbond_it1.274
r_scbond_other1.273
r_mcangle_other1.263
r_mcangle_it1.262
r_angle_refined_deg1.216
r_mcbond_it0.726
r_mcbond_other0.717
r_nbd_refined0.207
r_symmetry_nbd_other0.173
r_nbtor_refined0.172
r_symmetry_nbd_refined0.148
r_nbd_other0.136
r_xyhbond_nbd_refined0.103
r_symmetry_xyhbond_nbd_refined0.085
r_symmetry_nbtor_other0.082
r_chiral_restr0.068
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms923
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling