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Crystal Structure of the Plasmodium falciparum Bromodomain PfBDP1 in complex with RMM23
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 20% PEG MMW (PEG 2K, 3350, 4K and 5K MME ;each 12.5 %) ,7% (v/v) Tacsimate, 0.1 M HEPES pH 7.2
Crystal Properties Matthews coefficient Solvent content 2.88 57.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.12 α = 90 b = 88.215 β = 90 c = 108.493 γ = 90
Symmetry Space Group I 2 2 2
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 EIGER2 X CdTe 16M 2022-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.88560 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.787 35.965 91.8 0.07 0.076 0.999 13.4 6.3 9402
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.787 1.944 0.612
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 1.79 35.96 1.35 9398 433 52.79 0.2105 0.2089 0.2116 0.2432 0.2447 49.69
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 10.6619 f_angle_d 0.3931 f_chiral_restr 0.0349 f_plane_restr 0.0027 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1038 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 22
Software Software Software Name Purpose PHENIX refinement STARANISO data scaling PHASER phasing XDS data reduction