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Crystal structure of NudC from Mycobacterium abscessus in complex with AMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 10% PEG8000, 0.1 M imidazole pH 8.0, 0.2 M Ca(OAc)2
Crystal Properties Matthews coefficient Solvent content 3.15 60.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.999 α = 90 b = 131.999 β = 90 c = 174.314 γ = 120
Symmetry Space Group P 61 2 2
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 2023-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.9792 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.6 19.98 95.1 0.08 0.084 0.024 0.999 17.5 12 26851
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 90.8 1.02 1.079 0.343 0.705 9.6
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 2.6 19.98 25460 1347 95.01 0.22282 0.22043 0.2215 0.26882 0.2689 RANDOM 86.245
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] -0.09 -0.05 -0.09 0.3
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 14.114 r_long_range_B_other 14.093 r_dihedral_angle_3_deg 14.025 r_scangle_other 10.213 r_mcangle_it 9.9 r_mcangle_other 9.899 r_dihedral_angle_1_deg 7.434 r_mcbond_other 6.504 r_mcbond_it 6.503 r_scbond_it 6.458
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 14.114 r_long_range_B_other 14.093 r_dihedral_angle_3_deg 14.025 r_scangle_other 10.213 r_mcangle_it 9.9 r_mcangle_other 9.899 r_dihedral_angle_1_deg 7.434 r_mcbond_other 6.504 r_mcbond_it 6.503 r_scbond_it 6.458 r_scbond_other 6.456 r_dihedral_angle_2_deg 6.43 r_angle_refined_deg 1.265 r_angle_other_deg 0.452 r_chiral_restr 0.058 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 4540 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing XDS data reduction