6ZB1 | pdb_00006zb1

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH GSK620


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
2.2445.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.428α = 90
b = 71.855β = 90
c = 31.991γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002014-10-02MSINGLE 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)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
11.671.8695.80.017423.31588
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6883.20.05812.32

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 structure1.635.9531584180594.9990.1560.1540.170.18520.212.918
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]
-0.19-0.1420.332
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.946
r_dihedral_angle_4_deg23.347
r_dihedral_angle_3_deg12.773
r_lrange_it5.224
r_lrange_other5.222
r_dihedral_angle_1_deg4.837
r_scangle_it1.562
r_scangle_other1.561
r_mcangle_other1.435
r_mcangle_it1.433
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.946
r_dihedral_angle_4_deg23.347
r_dihedral_angle_3_deg12.773
r_lrange_it5.224
r_lrange_other5.222
r_dihedral_angle_1_deg4.837
r_scangle_it1.562
r_scangle_other1.561
r_mcangle_other1.435
r_mcangle_it1.433
r_angle_other_deg1.349
r_angle_refined_deg1.207
r_scbond_it0.902
r_scbond_other0.901
r_mcbond_it0.828
r_mcbond_other0.811
r_symmetry_xyhbond_nbd_other0.281
r_nbd_refined0.216
r_nbd_other0.178
r_symmetry_nbd_other0.175
r_nbtor_refined0.174
r_symmetry_nbd_refined0.169
r_xyhbond_nbd_refined0.114
r_symmetry_xyhbond_nbd_refined0.095
r_symmetry_nbtor_other0.079
r_chiral_restr0.066
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 Atoms919
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling