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Crystal structure of Candida glabrata Bdf1 bromodomain 2 bound to I-BET151
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Crystal structure of Bdf1 Bromodomain 2 from Candida glabrata in the unbound state
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.9 M Ammonium Sulfate, 0.1 M Sodium Cacodylate pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.65 66.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.588 α = 90 b = 88.426 β = 90 c = 257.785 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 4M 2018-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 55.2 47.4 0.292 0.99 6.7 7.4 28171 24.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.18 8.5 2.056 0.601 1.7 7.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.95 43.58 1.34 28164 1407 47.44 0.1974 0.1951 0.195 0.2405 0.2409 36.3
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 Key Refinement Restraint Deviation f_dihedral_angle_d 12.4055 f_angle_d 0.5501 f_chiral_restr 0.0418 f_plane_restr 0.0041 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3753 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 278
Software Software Software Name Purpose PHENIX refinement AutoProcess data reduction STARANISO data scaling MOLREP phasing