7NQ3 | pdb_00007nq3

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N4-((1R,5S,6r)-3-oxabicyclo[3.1.0]hexan-6-yl)-6-((S)-methoxy(phenyl)methyl)-N2-methylpyridine-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
2.2645.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.101α = 90
b = 52.529β = 90
c = 32.058γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002016-10-25MSINGLE 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
11.652.5394.20.0160.99743.12.915547
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)
11.61.6974.10.0460.97516.42

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-VALUE1.60342.4561545274192.9840.160.15780.170.19440.217.271
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]
-0.345-0.0160.361
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.411
r_dihedral_angle_4_deg19.783
r_dihedral_angle_3_deg11.668
r_lrange_it5.815
r_lrange_other5.813
r_dihedral_angle_1_deg4.801
r_scangle_it2.371
r_scangle_other2.37
r_mcangle_other2.03
r_mcangle_it2.028
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.411
r_dihedral_angle_4_deg19.783
r_dihedral_angle_3_deg11.668
r_lrange_it5.815
r_lrange_other5.813
r_dihedral_angle_1_deg4.801
r_scangle_it2.371
r_scangle_other2.37
r_mcangle_other2.03
r_mcangle_it2.028
r_scbond_it1.402
r_scbond_other1.4
r_angle_other_deg1.26
r_angle_refined_deg1.173
r_mcbond_it1.148
r_mcbond_other1.131
r_nbd_refined0.191
r_nbtor_refined0.168
r_symmetry_nbd_other0.161
r_nbd_other0.142
r_symmetry_nbd_refined0.101
r_xyhbond_nbd_refined0.097
r_symmetry_xyhbond_nbd_refined0.09
r_symmetry_nbtor_other0.078
r_chiral_restr0.061
r_symmetry_xyhbond_nbd_other0.051
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 Atoms928
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling