☰ Navigation Tabs
1.2 Angstrom Resolution Crystal Structure of Nucleoside Triphosphatase NudI from Klebsiella pneumoniae in Complex with HEPES
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 10.0 mg/mL protein, 0.5 M sodium chloride, 0.01 M Tris, pH 8.3 against Classics II (F8) (0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 25% w/v PEG3350)
Crystal Properties Matthews coefficient Solvent content 2.18 43.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.14 α = 77.07 b = 39.346 β = 80.74 c = 56.294 γ = 86.2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 C(111) 2018-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.2 30 92.3 0.07 0.07 0.088 0.052 13.7 2.8 78810 -3 12.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 91.1 0.79 0.79 0.973 0.563 0.593 2.1 2.9
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 SAD THROUGHOUT 1.2 27.14 74887 3897 92.16 0.15503 0.1534 0.1544 0.18662 0.1859 RANDOM 16.812
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] 0.05 0.61 -0.47 0.66 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.156 r_sphericity_free 16.896 r_rigid_bond_restr 11.074 r_dihedral_angle_4_deg 10.724 r_dihedral_angle_3_deg 10.458 r_sphericity_bonded 7.487 r_dihedral_angle_1_deg 5.562 r_long_range_B_refined 2.807 r_long_range_B_other 2.806 r_scangle_other 2.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.156 r_sphericity_free 16.896 r_rigid_bond_restr 11.074 r_dihedral_angle_4_deg 10.724 r_dihedral_angle_3_deg 10.458 r_sphericity_bonded 7.487 r_dihedral_angle_1_deg 5.562 r_long_range_B_refined 2.807 r_long_range_B_other 2.806 r_scangle_other 2.288 r_scbond_it 2 r_scbond_other 1.985 r_mcangle_it 1.614 r_mcangle_other 1.614 r_angle_refined_deg 1.4 r_mcbond_it 1.38 r_mcbond_other 1.374 r_angle_other_deg 0.505 r_chiral_restr 0.077 r_gen_planes_refined 0.04 r_gen_planes_other 0.037 r_bond_refined_d 0.008 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2312 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing