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CD-NTase EfCdnE in complex with intermediate pppU[2'-5']p
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 sodium tartrate, PEG 3350, MgCl2, UTP
Crystal Properties Matthews coefficient Solvent content 2.12 42.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.418 α = 90 b = 56.94 β = 97.019 c = 64.812 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 EIGER X 16M 2022-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 07A 0.97626 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 2.02 30 97.8 0.067 24.5 5.9 19291
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.09 94.8 0.162 6.2
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 2.021 28.486 19274 971 97.59 0.167 0.1651 0.1758 0.2102 0.1808 26.469
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] 0.013 -0.03 0.074 -0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.833 r_dihedral_angle_4_deg 22.336 r_dihedral_angle_3_deg 14.282 r_dihedral_angle_1_deg 6.72 r_lrange_it 5.614 r_lrange_other 5.578 r_scangle_other 4.324 r_scangle_it 4.309 r_mcangle_it 3.441 r_mcangle_other 3.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.833 r_dihedral_angle_4_deg 22.336 r_dihedral_angle_3_deg 14.282 r_dihedral_angle_1_deg 6.72 r_lrange_it 5.614 r_lrange_other 5.578 r_scangle_other 4.324 r_scangle_it 4.309 r_mcangle_it 3.441 r_mcangle_other 3.44 r_scbond_other 2.831 r_scbond_it 2.827 r_mcbond_it 2.383 r_mcbond_other 2.383 r_angle_refined_deg 1.453 r_angle_other_deg 1.363 r_nbd_other 0.267 r_symmetry_nbd_refined 0.218 r_nbd_refined 0.205 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.167 r_symmetry_xyhbond_nbd_other 0.162 r_xyhbond_nbd_refined 0.154 r_metal_ion_refined 0.107 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.072 r_bond_refined_d 0.011 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 2513 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing