☰ Navigation Tabs
Structure of methyltransferase domain of Spb1 boudn to SAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ELZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 20 mM Hepes KOH pH 8
150 mM KCl
0.5 mM TCEP
5% Glycerol
15% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.46 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.714 α = 90 b = 45.497 β = 123.422 c = 92.031 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r 2019-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.58 50 83.08 0.109 0.037 0.982 18.1 8.1 66501 14.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.61 0.037 0.497 0.93
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6ELZ 1.58 42.42 1.34 56274 1992 84.02 0.2297 0.2291 0.2304 0.2451 0.2457 RANDOM
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 19.9634 f_angle_d 1.0581 f_chiral_restr 0.0642 f_bond_d 0.0068 f_plane_restr 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3348 Nucleic Acid Atoms Solvent Atoms 541 Heterogen Atoms 54
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing