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Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with dATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other apo DwCdnB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 2 % v/v Tacsimate,
0.1 M Bis-Tris pH 6.5,
20 % w/v PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.31 46.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.355 α = 99.56 b = 46.614 β = 105.81 c = 59.644 γ = 100.12
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 EIGER2 X 9M 2021-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.99984 NSRRC TPS 05A
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 2.19 30 96.2 0.019 37.853 2.1 17231
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.28 95.5 0.995 2.2
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 2.19 22 16353 853 95.45 0.16521 0.16353 0.1736 0.19571 0.1895 RANDOM 34.384
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] 0.23 -0.03 0.1 0.06 -0.54 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.849 r_dihedral_angle_4_deg 18.348 r_dihedral_angle_3_deg 15.681 r_long_range_B_other 7.542 r_long_range_B_refined 7.534 r_dihedral_angle_1_deg 6.451 r_scangle_other 5.926 r_mcangle_it 4.64 r_mcangle_other 4.639 r_scbond_it 3.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.849 r_dihedral_angle_4_deg 18.348 r_dihedral_angle_3_deg 15.681 r_long_range_B_other 7.542 r_long_range_B_refined 7.534 r_dihedral_angle_1_deg 6.451 r_scangle_other 5.926 r_mcangle_it 4.64 r_mcangle_other 4.639 r_scbond_it 3.795 r_scbond_other 3.794 r_mcbond_it 3.104 r_mcbond_other 3.103 r_angle_refined_deg 1.403 r_angle_other_deg 0.962 r_chiral_restr 0.068 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 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 2627 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data scaling