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Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with UMPNPP
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 0.1 M Bis-Tris pH6.5,
20 % w/v PEG 5000 MME.
Crystal Properties Matthews coefficient Solvent content 2.34 47.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.346 α = 74.396 b = 46.244 β = 73.126 c = 61.058 γ = 84.271
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 2021-10-27 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 1.9 30 95 0.024 32.553 2.1 26385
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 1.9 1.97 0.972
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 MOLECULAR REPLACEMENT THROUGHOUT 1.903 28.287 26372 1381 94.263 0.173 0.1708 0.1818 0.2074 0.213 25.599
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] 0.163 -0.182 0.053 -0.079 0.127 -0.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.597 r_dihedral_angle_3_deg 15.068 r_dihedral_angle_4_deg 14.985 r_lrange_it 7.963 r_lrange_other 7.443 r_dihedral_angle_1_deg 6.68 r_scangle_it 5.34 r_scangle_other 4.569 r_mcangle_it 3.527 r_mcangle_other 3.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.597 r_dihedral_angle_3_deg 15.068 r_dihedral_angle_4_deg 14.985 r_lrange_it 7.963 r_lrange_other 7.443 r_dihedral_angle_1_deg 6.68 r_scangle_it 5.34 r_scangle_other 4.569 r_mcangle_it 3.527 r_mcangle_other 3.526 r_scbond_it 3.401 r_scbond_other 2.945 r_mcbond_it 2.415 r_mcbond_other 2.415 r_angle_refined_deg 1.431 r_angle_other_deg 1.338 r_nbd_refined 0.211 r_nbd_other 0.185 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.163 r_xyhbond_nbd_refined 0.158 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.013 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2616 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data scaling