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SlNDPS1-AtcPT4 Chimera complexed with GSPP, Mg2+, and IPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8KGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 PEG3350, malonate acid
Crystal Properties Matthews coefficient Solvent content 2.25 45.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.54 α = 90 b = 126.71 β = 90.25 c = 72.69 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 80 PIXEL DECTRIS EIGER X 9M 2022-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.32 50 99.9 0.109 0.998 11.17 5.9 275956
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.32 2.46 100 1.39 0.547 1.22 5.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.32 47.81 44269 2334 99.91 0.1905 0.18819 0.23518 0.233 RANDOM 53.356
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] 0.33 0.54 1.23 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.734 r_dihedral_angle_4_deg 23.743 r_dihedral_angle_3_deg 17.352 r_long_range_B_other 10.804 r_long_range_B_refined 10.801 r_scangle_other 7.878 r_mcangle_it 6.434 r_mcangle_other 6.434 r_dihedral_angle_1_deg 6.223 r_scbond_it 4.951
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.734 r_dihedral_angle_4_deg 23.743 r_dihedral_angle_3_deg 17.352 r_long_range_B_other 10.804 r_long_range_B_refined 10.801 r_scangle_other 7.878 r_mcangle_it 6.434 r_mcangle_other 6.434 r_dihedral_angle_1_deg 6.223 r_scbond_it 4.951 r_scbond_other 4.951 r_mcbond_it 4.253 r_mcbond_other 4.252 r_angle_other_deg 1.445 r_angle_refined_deg 1.347 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 7853 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement PHENIX refinement DIALS data reduction XDS data scaling PHASER phasing