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binary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other structure of apo SFM4-3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.2 M lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, and 28% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.94 58.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.61 α = 90 b = 65.628 β = 103.51 c = 107.378 γ = 90
Symmetry Space Group P 1 21 1
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 2021-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 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 50 98.8 0.135 0.148 0.06 0.974 4.3 6.1 55909
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 2.03 99.7 0.586 0.64 0.255 0.915 6.3
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 24.41 53014 2832 98.77 0.19347 0.19151 0.2012 0.2311 0.2324 RANDOM 36.354
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] 1.66 -1.33 3.74 -4.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.286 r_dihedral_angle_2_deg 12.959 r_long_range_B_refined 5.957 r_long_range_B_other 5.957 r_dihedral_angle_1_deg 5.837 r_scangle_other 4.326 r_mcangle_other 3.294 r_mcangle_it 3.293 r_scbond_it 2.843 r_scbond_other 2.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.286 r_dihedral_angle_2_deg 12.959 r_long_range_B_refined 5.957 r_long_range_B_other 5.957 r_dihedral_angle_1_deg 5.837 r_scangle_other 4.326 r_mcangle_other 3.294 r_mcangle_it 3.293 r_scbond_it 2.843 r_scbond_other 2.842 r_mcbond_it 2.282 r_mcbond_other 2.282 r_angle_refined_deg 1.363 r_angle_other_deg 0.386 r_chiral_restr 0.081 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 4315 Nucleic Acid Atoms 619 Solvent Atoms 346 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling HKL-3000 data reduction PHASER phasing