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Crystal structure of the SET domain of LSMT bound to MeLysine and AdoHcy
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MLV PDB ENTRY 1MLV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 0.95-1.10 M Sodium Acetate, 100 mM Methyllysine Acetate, 1 mM TCEP, 400 uM S-adenosylhomocysteine, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.2 70.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.41 α = 90 b = 153.19 β = 90 c = 266.32 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 95 IMAGE PLATE RIGAKU RAXIS IV Osmic Confocal Mirrors 2003-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.55 30 96.5 0.044 30.2 4.1 84637 83829 -3 -3 37.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.55 2.64 93.6 0.485 2.45 7768
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1MLV 2.55 29.65 83829 74004 3761 85.1 0.23 0.228 0.228 0.2284 0.269 0.2686 RANDOM 70.8
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] -26.08 35 -8.92
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.3 c_scangle_it 2.69 c_mcangle_it 2.33 c_scbond_it 1.65 c_mcbond_it 1.32 c_angle_deg 1.3 c_improper_angle_d 0.78 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10545 Nucleic Acid Atoms Solvent Atoms 652 Heterogen Atoms 111
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing