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The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-123
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9NIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 298 Ammonium Acetate, HEPES, Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 3.43 64.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.253 α = 90 b = 114.253 β = 90 c = 146.029 γ = 90
Symmetry Space Group P 41 21 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 EIGER2 XE 16M Rh coated collimating mirrors, K-B focusing mirrors 2024-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.73 1.85 SSRL BL12-2
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 2.41 57.13 99.87 0.07572 0.07745 0.01581 1 25.27 21.9 37632 69.67
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 2.41 2.496 99.01 2.685 2.856 0.9364 0.226 0.58 8.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.41 57.13 1.34 37632 1812 99.88 0.195 0.1938 0.1952 0.2195 0.2228 77.05
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.1181 f_angle_d 0.5429 f_chiral_restr 0.0389 f_plane_restr 0.0039 f_bond_d 0.0032
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4253 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 33
Software Software Software Name Purpose Coot model building PHENIX refinement autoPROC data reduction autoPROC data scaling PHASER phasing