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Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with GTP
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 0.2 M sodium formate, 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.04 39.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.033 α = 90 b = 100.404 β = 101.621 c = 46.398 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 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 2.17 30 99.3 0.028 47.211 4.2 16522
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 2.17 2.25 0.979
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 2.171 22.734 16498 824 99.356 0.243 0.2417 0.2461 0.2718 0.2852 37.635
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] -0.014 -0.022 -0.079 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.299 r_dihedral_angle_4_deg 18.475 r_dihedral_angle_3_deg 17.559 r_lrange_it 8.982 r_lrange_other 8.982 r_dihedral_angle_1_deg 8.126 r_mcangle_it 5.25 r_mcangle_other 5.249 r_scangle_it 4.702 r_scangle_other 4.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.299 r_dihedral_angle_4_deg 18.475 r_dihedral_angle_3_deg 17.559 r_lrange_it 8.982 r_lrange_other 8.982 r_dihedral_angle_1_deg 8.126 r_mcangle_it 5.25 r_mcangle_other 5.249 r_scangle_it 4.702 r_scangle_other 4.701 r_mcbond_it 3.349 r_mcbond_other 3.341 r_scbond_it 2.964 r_scbond_other 2.96 r_angle_refined_deg 1.393 r_angle_other_deg 1.244 r_nbd_other 0.237 r_symmetry_nbd_refined 0.223 r_nbd_refined 0.22 r_symmetry_xyhbond_nbd_refined 0.214 r_xyhbond_nbd_refined 0.207 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_other 0.168 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.06 r_bond_refined_d 0.008 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 2585 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data scaling