7OGY

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1-benzyl-N5-cyclopropyl-N3-methyl-1H-pyrazole-3,5-dicarboxamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin house structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29330% PEG 300, 0.1M MES buffer pH6.5
Crystal Properties
Matthews coefficientSolvent content
2.2545.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.851α = 90
b = 52.411β = 90
c = 32.066γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002015-08-28MSINGLE 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
11.671.85950.0130.99751.72.715652
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)
11.61.69770.0390.959201.8

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUEin house structure1.60214.1141554677593.9620.1590.15740.192114.576
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]
-0.195-0.2070.401
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.639
r_dihedral_angle_4_deg19.839
r_dihedral_angle_3_deg12.03
r_lrange_it5.53
r_lrange_other5.529
r_dihedral_angle_1_deg4.831
r_scangle_it2.277
r_scangle_other2.276
r_mcangle_it1.674
r_mcangle_other1.672
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.639
r_dihedral_angle_4_deg19.839
r_dihedral_angle_3_deg12.03
r_lrange_it5.53
r_lrange_other5.529
r_dihedral_angle_1_deg4.831
r_scangle_it2.277
r_scangle_other2.276
r_mcangle_it1.674
r_mcangle_other1.672
r_scbond_it1.344
r_scbond_other1.343
r_angle_other_deg1.243
r_angle_refined_deg1.152
r_mcbond_it0.955
r_mcbond_other0.954
r_nbd_refined0.193
r_nbd_other0.171
r_nbtor_refined0.165
r_symmetry_nbd_other0.163
r_symmetry_nbd_refined0.14
r_symmetry_xyhbond_nbd_refined0.107
r_xyhbond_nbd_refined0.105
r_symmetry_nbtor_other0.077
r_chiral_restr0.063
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 Atoms919
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling