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The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-I-86
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7RSP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 298 0.1 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 17% w/v Polyethylene glycol 10,000
Crystal Properties Matthews coefficient Solvent content 3.42 64.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.159 α = 90 b = 113.159 β = 90 c = 145.684 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 2024-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979460 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 2.01 61.25 94.74 0.1959 0.2003 0.04073 0.993 12.49 24 60721 42.95
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 2.01 2.082 6.429 6.584 1.366 0.0291 0.74 22.6
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 2.01 61.25 1.34 60260 3038 94.75 0.185 0.1835 0.1822 0.2117 0.2107 50.9
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 12.3277 f_angle_d 0.867 f_chiral_restr 0.0554 f_plane_restr 0.008 f_bond_d 0.0071
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4224 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 65
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction Coot model building autoPROC data scaling PHASER phasing