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SpnK Methyltransferase from the Spinosyn Biosynthetic Pathway in Complex with Mg
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 293 100 mM Sodium citrate, pH 6.3, 34% v/v PEG 200, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.09 69.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.114 α = 90 b = 134.114 β = 90 c = 159.718 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS3 6M 2021-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.5 50 100 0.129 5.1 12.6 51119
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 100 0.796 12.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 2.5 47.46 47477 2606 97.93 0.20964 0.20783 0.2121 0.24327 0.2434 RANDOM 39.812
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] 0.41 0.41 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.332 r_dihedral_angle_4_deg 17.361 r_dihedral_angle_3_deg 13.759 r_long_range_B_other 10.659 r_long_range_B_refined 10.656 r_scangle_other 7.005 r_mcangle_other 6.238 r_mcangle_it 6.229 r_dihedral_angle_1_deg 5.97 r_scbond_it 4.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.332 r_dihedral_angle_4_deg 17.361 r_dihedral_angle_3_deg 13.759 r_long_range_B_other 10.659 r_long_range_B_refined 10.656 r_scangle_other 7.005 r_mcangle_other 6.238 r_mcangle_it 6.229 r_dihedral_angle_1_deg 5.97 r_scbond_it 4.291 r_scbond_other 4.291 r_mcbond_it 3.959 r_mcbond_other 3.903 r_angle_refined_deg 1.237 r_angle_other_deg 1.175 r_chiral_restr 0.054 r_gen_planes_refined 0.022 r_gen_planes_other 0.007 r_bond_refined_d 0.006 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5869 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing