7NPZ

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH (R)-N5-cyclopropyl-N3-methyl-2-oxo-1-(1-phenylethyl)-1,2-dihydropyridine-3,5-dicarboxamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin house

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.529330% PEG 300, 0.1M MES buffer pH6.5
Crystal Properties
Matthews coefficientSolvent content
2.2445.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.86α = 90
b = 52.31β = 90
c = 31.97γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.2835.9396.80.99815.14.430641
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.281.3184.80.4921.62.6

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 house1.2835.9330594154296.1410.1750.17360.193319.46
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]
0.0050.003-0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.727
r_dihedral_angle_4_deg19.301
r_dihedral_angle_3_deg11.576
r_lrange_it5.097
r_lrange_other5.095
r_dihedral_angle_1_deg4.916
r_scangle_it2.157
r_scangle_other2.155
r_mcangle_other1.436
r_mcangle_it1.434
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.727
r_dihedral_angle_4_deg19.301
r_dihedral_angle_3_deg11.576
r_lrange_it5.097
r_lrange_other5.095
r_dihedral_angle_1_deg4.916
r_scangle_it2.157
r_scangle_other2.155
r_mcangle_other1.436
r_mcangle_it1.434
r_angle_other_deg1.36
r_scbond_it1.296
r_scbond_other1.294
r_angle_refined_deg1.202
r_mcbond_it0.845
r_mcbond_other0.835
r_nbd_refined0.206
r_nbtor_refined0.174
r_symmetry_nbd_other0.164
r_nbd_other0.162
r_symmetry_nbd_refined0.121
r_symmetry_nbtor_other0.082
r_xyhbond_nbd_refined0.082
r_chiral_restr0.066
r_symmetry_xyhbond_nbd_refined0.052
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms914
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling