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Crystal structure of SkABA3 from Shimazuella kribbensis in complex with PPi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ZAF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.55 M Sodium chloride, 0.1 M Bis-Tris 6.5, 23% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 1.97 37.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.249 α = 90 b = 64.607 β = 108.93 c = 70.955 γ = 90
Symmetry Space Group C 1 2 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 CCD RAYONIX MX300-HS 2023-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.9998 NSRRC TPS 05A
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 1.6 25 99.4 0.026 0.029 0.013 0.998 18.6 4.6 48426
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 1.6 1.66 99.7 0.097 0.11 0.051 0.993 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 8ZAF 1.6 23.28 45993 2433 99.25 0.18349 0.18137 0.191 0.22388 0.2313 RANDOM 17.777
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] -0.11 -0.88 0.94 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.156 r_dihedral_angle_4_deg 17.979 r_dihedral_angle_3_deg 14.487 r_dihedral_angle_1_deg 6.295 r_long_range_B_refined 5.525 r_long_range_B_other 5.454 r_scangle_other 3.764 r_mcangle_other 2.739 r_mcangle_it 2.736 r_scbond_it 2.468
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.156 r_dihedral_angle_4_deg 17.979 r_dihedral_angle_3_deg 14.487 r_dihedral_angle_1_deg 6.295 r_long_range_B_refined 5.525 r_long_range_B_other 5.454 r_scangle_other 3.764 r_mcangle_other 2.739 r_mcangle_it 2.736 r_scbond_it 2.468 r_scbond_other 2.467 r_angle_refined_deg 1.954 r_mcbond_it 1.83 r_mcbond_other 1.824 r_angle_other_deg 1.543 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 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 2911 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing