7OE5

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N5-hydroxycyclohexyl-N3-methyl-1-phenylethyl-1H-pyrazole-3,5-dicarboxamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin house

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29830% PEG 300, 0.1M MES buffer pH6.5
Crystal Properties
Matthews coefficientSolvent content
2.2545.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.786α = 90
b = 52.335β = 90
c = 32.174γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002016-12-18MSINGLE 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
11.632.1794.90.0270.99926.42.815655
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)
11.61.6979.20.3060.5153.51.9

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUEin house1.60227.4091560178094.1460.1650.16410.187918.987
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]
-0.595-0.3210.915
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.592
r_dihedral_angle_4_deg18.821
r_dihedral_angle_3_deg11.568
r_lrange_it5.044
r_lrange_other4.88
r_dihedral_angle_1_deg4.869
r_scangle_it3.148
r_scangle_other3.145
r_mcangle_other2.031
r_mcangle_it2.029
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.592
r_dihedral_angle_4_deg18.821
r_dihedral_angle_3_deg11.568
r_lrange_it5.044
r_lrange_other4.88
r_dihedral_angle_1_deg4.869
r_scangle_it3.148
r_scangle_other3.145
r_mcangle_other2.031
r_mcangle_it2.029
r_scbond_it1.871
r_scbond_other1.869
r_angle_other_deg1.244
r_mcbond_it1.199
r_angle_refined_deg1.183
r_mcbond_other1.176
r_symmetry_nbd_refined0.267
r_nbd_refined0.196
r_nbtor_refined0.166
r_nbd_other0.165
r_symmetry_nbd_other0.163
r_symmetry_xyhbond_nbd_refined0.153
r_xyhbond_nbd_refined0.127
r_symmetry_nbtor_other0.077
r_chiral_restr0.062
r_xyhbond_nbd_other0.006
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 Atoms121
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling