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Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with ATP (form 1)
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 pH 5.5, 25 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 46.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.343 α = 99.69 b = 46.559 β = 106.07 c = 59.78 γ = 99.37
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 2.25 30 94.2 0.018 41.309 2.1 15717
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 2.25 2.33 95.8 0.996 2.1
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 2.25 28 14885 832 94.05 0.17078 0.16855 0.1783 0.21217 0.22 RANDOM 36.266
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] 0.37 -0.05 0.15 -0.17 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.339 r_dihedral_angle_4_deg 18.533 r_dihedral_angle_3_deg 15.743 r_long_range_B_refined 7.045 r_long_range_B_other 7.039 r_dihedral_angle_1_deg 6.522 r_scangle_other 5.665 r_mcangle_it 4.298 r_mcangle_other 4.298 r_scbond_it 3.798
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.339 r_dihedral_angle_4_deg 18.533 r_dihedral_angle_3_deg 15.743 r_long_range_B_refined 7.045 r_long_range_B_other 7.039 r_dihedral_angle_1_deg 6.522 r_scangle_other 5.665 r_mcangle_it 4.298 r_mcangle_other 4.298 r_scbond_it 3.798 r_scbond_other 3.797 r_mcbond_it 2.954 r_mcbond_other 2.952 r_angle_refined_deg 1.387 r_angle_other_deg 0.917 r_chiral_restr 0.066 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 2625 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data scaling