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The structure of human vacuolar protein sorting 34 catalytic domain bound to RD-I-53
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 20% PEG, 0.2M MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.44 64.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.506 α = 90 b = 113.506 β = 90 c = 145.235 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 2023-12-19 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 2.16 53.85 99.98 0.1164 0.1185 0.02246 1 13.99 27.5 51494 56.6
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 2.16 2.237 99.98 3.425 3.486 0.6498 0.48 0.99 28.5
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 2.16 53.85 1.35 51488 2502 99.99 0.2082 0.2067 0.2082 0.2374 0.2386 72.69
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 13.8431 f_angle_d 0.7267 f_chiral_restr 0.0486 f_bond_d 0.0055 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4095 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 54
Software Software Software Name Purpose PHENIX refinement Coot model building autoPROC data reduction autoPROC data scaling PHASER phasing