7NPY | pdb_00007npy

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 6-benzyl-N2-methyl-N4-((1S,2S)-2-methylcyclopropyl)pyridine-2,4-dicarboxamide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29330% PEG 300, 0.1M MES buffer pH6.5
Crystal Properties
Matthews coefficientSolvent content
2.2545.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.047α = 90
b = 52.31β = 90
c = 32.087γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU2014-09-25MSINGLE 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
11.652.3195.50.0180.99936.82.915851
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)
11.61.6975.20.0940.899.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE1.60114.6561575277494.8290.1470.14590.160.17310.1820.646
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]
-0.249-0.1920.441
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.057
r_dihedral_angle_4_deg20.322
r_dihedral_angle_3_deg10.917
r_lrange_it5.208
r_lrange_other5.009
r_dihedral_angle_1_deg4.731
r_scangle_it2.54
r_scangle_other2.538
r_mcangle_other1.804
r_mcangle_it1.797
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.057
r_dihedral_angle_4_deg20.322
r_dihedral_angle_3_deg10.917
r_lrange_it5.208
r_lrange_other5.009
r_dihedral_angle_1_deg4.731
r_scangle_it2.54
r_scangle_other2.538
r_mcangle_other1.804
r_mcangle_it1.797
r_scbond_it1.511
r_scbond_other1.51
r_angle_other_deg1.34
r_angle_refined_deg1.235
r_mcbond_it1.064
r_mcbond_other1.01
r_nbd_refined0.208
r_nbtor_refined0.174
r_symmetry_nbd_other0.169
r_symmetry_nbd_refined0.165
r_nbd_other0.121
r_xyhbond_nbd_refined0.094
r_symmetry_xyhbond_nbd_refined0.082
r_symmetry_nbtor_other0.08
r_chiral_restr0.067
r_symmetry_xyhbond_nbd_other0.017
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms912
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling