7OES | pdb_00007oes

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1,5-dimethyl-N-(2-(methylamino)-2-oxoethyl)-6-oxo-N-(2-phenylpropyl)-1,6-dihydropyridine-3-carboxamide


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
2.2344.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.647α = 90
b = 52.388β = 90
c = 31.987γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002016-10-25MSINGLE 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
11.642.2994.60.0170.99633.12.415516
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)
11.61.69710.0660.92410.21.7

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 structure1.60232.0071540274193.5890.1560.15490.170.18320.1920.022
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]
-0.078-0.2910.369
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.623
r_dihedral_angle_4_deg21.243
r_dihedral_angle_3_deg12.41
r_lrange_it5.73
r_lrange_other5.728
r_dihedral_angle_1_deg4.755
r_scangle_it2.855
r_scangle_other2.854
r_mcangle_other1.877
r_mcangle_it1.873
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.623
r_dihedral_angle_4_deg21.243
r_dihedral_angle_3_deg12.41
r_lrange_it5.73
r_lrange_other5.728
r_dihedral_angle_1_deg4.755
r_scangle_it2.855
r_scangle_other2.854
r_mcangle_other1.877
r_mcangle_it1.873
r_scbond_it1.752
r_scbond_other1.751
r_angle_other_deg1.224
r_angle_refined_deg1.176
r_mcbond_it1.093
r_mcbond_other1.073
r_nbd_refined0.194
r_nbtor_refined0.166
r_symmetry_nbd_other0.165
r_nbd_other0.146
r_symmetry_nbd_refined0.14
r_xyhbond_nbd_refined0.103
r_symmetry_xyhbond_nbd_refined0.088
r_symmetry_nbtor_other0.078
r_chiral_restr0.061
r_gen_planes_refined0.004
r_bond_refined_d0.003
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 Atoms185
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling