☰ Navigation Tabs
Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB Ear-cut mutant in complex with ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8YSN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M Bis-Tris pH 6.5,
0.2 M Sodium fluoride,
23 % w/v PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.31 46.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.331 α = 90 b = 72.832 β = 90 c = 100.998 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 EIGER2 X 16M 2022-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 07A 0.97625 NSRRC TPS 07A
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 1.68 30 99.4 0.058 47.067 12 42038
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 1.68 1.74 0.917
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 1.68 23.973 41873 2118 99.056 0.172 0.1709 0.1829 0.1994 0.2099 16.584
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] 0.166 0.11 -0.276
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.933 r_dihedral_angle_4_deg 15.4 r_dihedral_angle_3_deg 12.471 r_dihedral_angle_1_deg 6.649 r_lrange_it 5.826 r_lrange_other 5.67 r_scangle_it 4.305 r_scangle_other 4.279 r_mcangle_it 2.741 r_mcangle_other 2.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.933 r_dihedral_angle_4_deg 15.4 r_dihedral_angle_3_deg 12.471 r_dihedral_angle_1_deg 6.649 r_lrange_it 5.826 r_lrange_other 5.67 r_scangle_it 4.305 r_scangle_other 4.279 r_mcangle_it 2.741 r_mcangle_other 2.741 r_scbond_it 2.736 r_scbond_other 2.722 r_mcbond_it 1.761 r_mcbond_other 1.749 r_angle_other_deg 1.401 r_angle_refined_deg 1.381 r_nbd_other 0.23 r_symmetry_nbd_refined 0.22 r_nbd_refined 0.212 r_symmetry_xyhbond_nbd_refined 0.201 r_xyhbond_nbd_refined 0.181 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.173 r_chiral_restr 0.078 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2474 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data scaling