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SAH-bound C-Methyltransferase Fur6 from Streptomyces sp. KO-3988
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 PEG3350, calcium hydroxide, HEPES-NaOH
Crystal Properties Matthews coefficient Solvent content 2.81 56.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.98 α = 90 b = 91.84 β = 90 c = 125.35 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 EIGER X 9M 2020-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.000 SPring-8 BL32XU
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 2.12 50 100 0.984 5.93 8.1 94785
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.18 0.687 0.813
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 2.12 48.134 49768 2462 99.878 0.214 0.2115 0.2151 0.2561 0.2577 38.05
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] 0.39 1.274 -1.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.817 r_dihedral_angle_4_deg 16.228 r_dihedral_angle_3_deg 14.077 r_dihedral_angle_1_deg 6.57 r_lrange_it 4.402 r_lrange_other 4.4 r_scangle_it 3.291 r_scangle_other 3.291 r_mcangle_it 2.738 r_mcangle_other 2.738
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.817 r_dihedral_angle_4_deg 16.228 r_dihedral_angle_3_deg 14.077 r_dihedral_angle_1_deg 6.57 r_lrange_it 4.402 r_lrange_other 4.4 r_scangle_it 3.291 r_scangle_other 3.291 r_mcangle_it 2.738 r_mcangle_other 2.738 r_scbond_it 2.074 r_scbond_other 2.073 r_mcbond_it 1.866 r_mcbond_other 1.866 r_angle_refined_deg 1.3 r_angle_other_deg 1.198 r_nbd_other 0.208 r_nbd_refined 0.189 r_symmetry_nbd_other 0.164 r_symmetry_xyhbond_nbd_refined 0.157 r_nbtor_refined 0.151 r_symmetry_nbd_refined 0.137 r_xyhbond_nbd_refined 0.13 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.057 r_symmetry_xyhbond_nbd_other 0.009 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5303 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling CRANK2 phasing