8R6N

Crystal structure of Candida glabrata Bdf1 bromodomain 2 bound to a pyridoindole ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherCrystal structure of Bdf1 Bromodomain 2 from Candida glabrata in the unbound state

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.8 M sodium dihydrogen phosphate, 0.8 M potassium dihydrogen phosphate, 0.1 M Hepes pH 7.5
Crystal Properties
Matthews coefficientSolvent content
3.1761.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.582α = 90
b = 67.582β = 90
c = 152.83γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2018-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.9660ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.1161.8154.690.2770.9978.312.3578125.33
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.112.428.91.2660.696

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.1161.811.37578129554.690.25930.25740.28741.94
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.6107
f_angle_d0.6774
f_chiral_restr0.0427
f_plane_restr0.0052
f_bond_d0.0031
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms950
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms31

Software

Software
Software NamePurpose
PHENIXrefinement
AutoProcessdata reduction
STARANISOdata scaling
MOLREPphasing