6NEY

Crystal structure of TcBDF5, a bromodomain containing protein from Trypanosoma cruzi


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TCM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52921.8 M NH4SO4, 0.2 M Na Acetate and 0.1M Hepes pH7.5
Crystal Properties
Matthews coefficientSolvent content
1.9336.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.887α = 90
b = 70.428β = 90
c = 26.644γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97918APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.685098.20.0820.0870.036.67.813782
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.681.7183.70.7320.7890.2830.7496

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5TCM1.6846.491300467598.380.226030.223740.26702RANDOM26.064
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]
-2.082.46-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.278
r_dihedral_angle_4_deg14.422
r_dihedral_angle_3_deg14.085
r_dihedral_angle_1_deg6.292
r_long_range_B_refined4.414
r_long_range_B_other4.412
r_scangle_other3.532
r_mcangle_it2.782
r_mcangle_other2.78
r_scbond_it2.382
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.278
r_dihedral_angle_4_deg14.422
r_dihedral_angle_3_deg14.085
r_dihedral_angle_1_deg6.292
r_long_range_B_refined4.414
r_long_range_B_other4.412
r_scangle_other3.532
r_mcangle_it2.782
r_mcangle_other2.78
r_scbond_it2.382
r_scbond_other2.38
r_mcbond_it1.865
r_mcbond_other1.865
r_angle_refined_deg1.502
r_angle_other_deg1.388
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms951
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-3000data reduction