6ZB2

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH GSK549


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin house structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.529330% PEG 300, 0.1M MES buffer pH6.5
Crystal Properties
Matthews coefficientSolvent content
2.2545.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.017α = 90
b = 52.327β = 90
c = 32.033γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002015-03-25MSINGLE 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
12.2842.3398.40.270.98126.42.75759
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)
12.2842.3399.60.0650.94313.82.7

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUEin house structure2.28242.33565225896.1060.1430.13930.233923.693
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]
0.042-0.023-0.019
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.606
r_dihedral_angle_4_deg19.525
r_dihedral_angle_3_deg14.986
r_lrange_it7.019
r_lrange_other7.016
r_dihedral_angle_1_deg5.56
r_scangle_it4.296
r_scangle_other4.293
r_mcangle_it3.183
r_mcangle_other3.181
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.606
r_dihedral_angle_4_deg19.525
r_dihedral_angle_3_deg14.986
r_lrange_it7.019
r_lrange_other7.016
r_dihedral_angle_1_deg5.56
r_scangle_it4.296
r_scangle_other4.293
r_mcangle_it3.183
r_mcangle_other3.181
r_scbond_it2.609
r_scbond_other2.607
r_mcbond_it1.946
r_mcbond_other1.909
r_angle_refined_deg1.475
r_angle_other_deg1.243
r_symmetry_xyhbond_nbd_refined0.272
r_xyhbond_nbd_refined0.197
r_nbd_refined0.195
r_nbd_other0.185
r_symmetry_nbd_other0.175
r_nbtor_refined0.168
r_symmetry_nbd_refined0.145
r_symmetry_nbtor_other0.082
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms928
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling