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Crystal Structure of Histone-lysine N-methyltransferase from Leishmania major in complex with S-ADENOSYLMETHIONINE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q4QIU2-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 27.5% PEG 3350, 0.1M Bis-Tris 5.5, 0.2M NaCl. LemaA.18205.a.B2.PW39520 at 12.4 mg/mL. Crystals soaked with 5 mM SAM, plate 21007 C10 drop 2, Puck: PSL-2811, Cryo: 33% P3350, 0.1M BT 5.5, 0.2M NaCl
Crystal Properties Matthews coefficient Solvent content 2.16 43.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.816 α = 90 b = 91.915 β = 102.67 c = 81.797 γ = 90
Symmetry Space Group P 1 21 1
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 XE 9M 2026-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
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 1.93 49.37 99.9 0.145 0.157 0.06 0.997 8.1 6.8 75739
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 1.93 1.97 99.9 1.095 1.21 0.504 0.728 5.6
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 1.93 49.37 1.34 75562 3706 99.71 0.1851 0.1826 0.1902 0.2313 0.2331
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 15.733 f_angle_d 0.914 f_chiral_restr 0.051 f_plane_restr 0.011 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8067 Nucleic Acid Atoms Solvent Atoms 604 Heterogen Atoms 181
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction