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Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with CTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8YSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M BIS-TRIS propane pH 9.0,
30% w/v Polyethylene glycol 6,000.
Crystal Properties Matthews coefficient Solvent content 2.32 47.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.363 α = 90 b = 111.506 β = 100.415 c = 46.981 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 EIGER2 X 16M 2022-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 07A 0.97624 NSRRC TPS 07A
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 1.94 30 98.2 0.995 15.424 6.5 25742
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 1.94 2.01 0.705
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 1.944 23.881 25173 1245 95.635 0.204 0.2021 0.2087 0.2389 0.2245 26.792
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] -0.01 0.269 -0.032 -0.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.034 r_dihedral_angle_3_deg 14.941 r_dihedral_angle_4_deg 13.682 r_lrange_it 8.356 r_lrange_other 8.335 r_dihedral_angle_1_deg 6.658 r_scangle_it 4.909 r_scangle_other 4.908 r_mcangle_other 3.413 r_mcangle_it 3.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.034 r_dihedral_angle_3_deg 14.941 r_dihedral_angle_4_deg 13.682 r_lrange_it 8.356 r_lrange_other 8.335 r_dihedral_angle_1_deg 6.658 r_scangle_it 4.909 r_scangle_other 4.908 r_mcangle_other 3.413 r_mcangle_it 3.412 r_scbond_it 3.024 r_scbond_other 2.887 r_mcbond_it 2.207 r_mcbond_other 2.193 r_angle_refined_deg 1.444 r_angle_other_deg 1.314 r_nbd_other 0.257 r_symmetry_xyhbond_nbd_refined 0.246 r_nbd_refined 0.22 r_symmetry_nbd_other 0.192 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.168 r_symmetry_nbd_refined 0.155 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2647 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data scaling