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Crystal structure of Candida glabrata Bdf1 bromodomain 1 bound to a pyrazole ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Crystal structure of Candida glabrata Bdf1 bromodomain 1 in the unbound state
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 26% PEG 10000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate (pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.11 41.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.841 α = 90 b = 142.619 β = 90 c = 93.549 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 PILATUS3 2M 2018-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9660 ESRF MASSIF-1
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 1.82 39.11 99.1 0.116 0.996 10.4 4.1 20025 22.95
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 1.82 1.86 99.6 0.99 0.532 1.7 3.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.82 39.11 1.35 19990 1001 98.62 0.2006 0.1988 0.2342 0.2231 31.48
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 13.7586 f_angle_d 0.6056 f_chiral_restr 0.0399 f_plane_restr 0.004 f_bond_d 0.0033
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1780 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling MOLREP phasing