8YME | pdb_00008yme

BRD4-BD1 in complex with N-cyclohexyl-1-methyl-6-{[5-methyl-7-(1-methylpyrazol-3-yl)-4-oxo-pyrazolo[4,3-c]pyridin-2-yl]methyl}azepan-1-ium-4-carboxamide 2,2,2-trifluoroacetate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6CZU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72930.1M Hepes pH 7.0, 5% MgCl2, 20% PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.1242.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.05α = 90
b = 49.35β = 90
c = 61.06γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2022-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU1.0SPring-8BL45XU

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
11.18501000.99810.9414.743571
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)
11.181.250.524

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 DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.1838.38143508222099.9430.1580.15670.16550.18560.188321.222
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]
0.799-0.578-0.221
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.447
r_dihedral_angle_4_deg12.131
r_rigid_bond_restr11.915
r_dihedral_angle_3_deg11.539
r_dihedral_angle_1_deg5.484
r_lrange_it3.871
r_lrange_other3.863
r_scangle_it3.747
r_scangle_other3.698
r_scbond_it3.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.447
r_dihedral_angle_4_deg12.131
r_rigid_bond_restr11.915
r_dihedral_angle_3_deg11.539
r_dihedral_angle_1_deg5.484
r_lrange_it3.871
r_lrange_other3.863
r_scangle_it3.747
r_scangle_other3.698
r_scbond_it3.26
r_scbond_other3.242
r_mcbond_other2.54
r_mcbond_it2.537
r_mcangle_it2.489
r_mcangle_other2.487
r_angle_other_deg2.186
r_angle_refined_deg1.906
r_symmetry_nbd_refined0.347
r_nbd_other0.28
r_nbd_refined0.275
r_symmetry_nbd_other0.231
r_nbtor_refined0.187
r_xyhbond_nbd_refined0.156
r_symmetry_xyhbond_nbd_refined0.151
r_symmetry_xyhbond_nbd_other0.141
r_chiral_restr0.121
r_symmetry_nbtor_other0.078
r_bond_other_d0.031
r_gen_planes_other0.02
r_bond_refined_d0.015
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1047
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing