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SgvM methyltransferase with SAH and alpha-ketoleucine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model 8FTR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 283 PEG 3350 pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.95 58.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.347 α = 90 b = 68.347 β = 90 c = 186.207 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 IMAGE PLATE MAR scanner 300 mm plate 2021-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97856 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 38.133 99.4 0.113 0.999 15.8 21.7 23134
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.207 1.823 0.792
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 2.2 25 21977 1142 99.26 0.21282 0.2111 0.2177 0.2459 0.25 RANDOM 62.487
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] 0.66 0.66 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.347 r_dihedral_angle_3_deg 16.931 r_dihedral_angle_4_deg 13.466 r_long_range_B_refined 8.391 r_dihedral_angle_1_deg 6.333 r_mcangle_it 5.033 r_scbond_it 3.913 r_mcbond_it 3.289 r_angle_refined_deg 1.155 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.347 r_dihedral_angle_3_deg 16.931 r_dihedral_angle_4_deg 13.466 r_long_range_B_refined 8.391 r_dihedral_angle_1_deg 6.333 r_mcangle_it 5.033 r_scbond_it 3.913 r_mcbond_it 3.289 r_angle_refined_deg 1.155 r_chiral_restr 0.109 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2546 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing