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PsiM N247M in complex with SAH and norbaeocystin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 100 mM Tris HCl pH 8.5, 20% PEG 8000, 200 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.26 45.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.372 α = 90 b = 78.543 β = 90 c = 83.767 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 EIGER2 X CdTe 16M 2023-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.7293 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 0.9 18.49 98.99 0.997 11.31 13.5 238138 9.63
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 0.9 0.932 0.4
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 0.9 18.49 1.34 237900 1986 99.01 0.1379 0.1378 0.1387 0.1481 0.1488
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 7.643 f_angle_d 1.406 f_chiral_restr 0.112 f_bond_d 0.015 f_plane_restr 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2497 Nucleic Acid Atoms Solvent Atoms 437 Heterogen Atoms 45
Software Software Software Name Purpose PHENIX refinement xia2 data reduction DIALS data scaling PHASER phasing