7OER | pdb_00007oer

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N-(2,2-diphenylethyl)-1,5-dimethyl-N-(2-(methylamino)-2-oxoethyl)-6-oxo-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
2.2645.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.101α = 90
b = 52.536β = 90
c = 32.06γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002016-02-04MSINGLE 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
11.652.5494.40.0230.99526.92.815685
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)
11.61.69750.1550.6295.51.9

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 structure1.60229.7251553677293.3260.1560.15480.170.1790.1920.415
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]
0.111-0.3840.273
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.297
r_dihedral_angle_4_deg19.377
r_dihedral_angle_3_deg11.066
r_lrange_it5.779
r_lrange_other5.504
r_dihedral_angle_1_deg4.783
r_scangle_it3.169
r_scangle_other3.167
r_mcangle_it1.985
r_mcangle_other1.983
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.297
r_dihedral_angle_4_deg19.377
r_dihedral_angle_3_deg11.066
r_lrange_it5.779
r_lrange_other5.504
r_dihedral_angle_1_deg4.783
r_scangle_it3.169
r_scangle_other3.167
r_mcangle_it1.985
r_mcangle_other1.983
r_scbond_it1.884
r_scbond_other1.883
r_angle_other_deg1.242
r_mcbond_it1.175
r_mcbond_other1.174
r_angle_refined_deg1.166
r_nbd_refined0.194
r_nbtor_refined0.17
r_symmetry_nbd_other0.164
r_symmetry_xyhbond_nbd_refined0.139
r_nbd_other0.123
r_xyhbond_nbd_refined0.122
r_symmetry_nbd_refined0.114
r_symmetry_nbtor_other0.076
r_chiral_restr0.062
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 Atoms910
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling