6ZB0 | pdb_00006zb0

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1-benzyl-N-methyl-2-oxo-1,2-dihydropyridine-3-carboxamide


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
2.2946.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.106α = 90
b = 52.758β = 90
c = 32.318γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002014-08-07MSINGLE 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
11.6136.0595.50.01931.92.715692
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)
11.611.781.80.06511.21.8

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 structure1.61329.4911564778794.7210.1410.13930.150.17750.1914.632
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]
0.0120.017-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.653
r_dihedral_angle_4_deg23.709
r_dihedral_angle_3_deg12.475
r_lrange_it5.912
r_lrange_other5.91
r_dihedral_angle_1_deg5.334
r_scangle_it2.206
r_scangle_other2.204
r_mcangle_other1.509
r_mcangle_it1.506
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.653
r_dihedral_angle_4_deg23.709
r_dihedral_angle_3_deg12.475
r_lrange_it5.912
r_lrange_other5.91
r_dihedral_angle_1_deg5.334
r_scangle_it2.206
r_scangle_other2.204
r_mcangle_other1.509
r_mcangle_it1.506
r_angle_other_deg1.409
r_scbond_other1.345
r_scbond_it1.343
r_angle_refined_deg1.325
r_mcbond_it0.906
r_mcbond_other0.835
r_nbd_refined0.214
r_nbtor_refined0.178
r_symmetry_nbd_other0.174
r_nbd_other0.139
r_symmetry_nbd_refined0.124
r_xyhbond_nbd_refined0.118
r_symmetry_xyhbond_nbd_refined0.114
r_symmetry_nbtor_other0.081
r_chiral_restr0.079
r_gen_planes_refined0.007
r_bond_refined_d0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms941
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling