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Crystal Structure of the Leishmania Bromodomain LmxBDF5.1 in complex with OXFBD06
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 0.1 M Potassium thiocyanate, 30% PEG monomethyl ether 2,000
Crystal Properties Matthews coefficient Solvent content 1.89 34.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.794 α = 90 b = 49.646 β = 90 c = 85.634 γ = 90
Symmetry Space Group P 21 21 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 2023-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.96770 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.45 44.79 99.9 0.109 0.115 0.035 0.998 12.6 10.4 34606
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) Redundancy Number Unique Reflections (All) 1 1.45 1.47 100 1.205 1.266 0.382 0.823 10.7
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 1.45 42.95 1.34 34538 1710 99.85 0.1381 0.1364 0.1698 0.1698
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 16.664 f_angle_d 0.697 f_chiral_restr 0.072 f_plane_restr 0.007 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1752 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 83
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHASER phasing XDS data reduction PDB_EXTRACT data extraction