☰ Navigation Tabs
SpnK Methyltransferase from the Spinosyn Biosynthetic Pathway in Complex with SAH
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 4.11 70.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.975 α = 90 b = 133.975 β = 90 c = 160.109 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 2021-05-27 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) 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 2.1 50 100 0.096 0.101 0.029 0.996 5.7 11.5 85935
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 2.1 2.14 100 0.898 0.938 0.268 0.857 11.9
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 2.1 49.63 80023 4225 98.77 0.20263 0.20131 0.2152 0.22781 0.2353 RANDOM 29.584
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] 0.34 0.34 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.282 r_dihedral_angle_4_deg 18.033 r_dihedral_angle_3_deg 14.995 r_dihedral_angle_1_deg 8.166 r_long_range_B_refined 7.064 r_long_range_B_other 7.043 r_scangle_other 3.75 r_mcangle_it 3.512 r_mcangle_other 3.511 r_scbond_it 2.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.282 r_dihedral_angle_4_deg 18.033 r_dihedral_angle_3_deg 14.995 r_dihedral_angle_1_deg 8.166 r_long_range_B_refined 7.064 r_long_range_B_other 7.043 r_scangle_other 3.75 r_mcangle_it 3.512 r_mcangle_other 3.511 r_scbond_it 2.333 r_scbond_other 2.333 r_mcbond_it 2.148 r_mcbond_other 2.148 r_angle_refined_deg 2.078 r_angle_other_deg 1.499 r_chiral_restr 0.093 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5924 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing