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Crystal structure of Vps17p PX from S. cerevisiae (Space)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 7.5 293 1.5M lithium sulfate, 0.1 M HEPES-Na, under a microgravity environment
Crystal Properties Matthews coefficient Solvent content 2.6 56.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.28 α = 90 b = 100.28 β = 90 c = 100.28 γ = 90
Symmetry Space Group P 21 3
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 ADSC QUANTUM 4 2004-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 1.000 SPring-8 BL12B2
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 2.02 44.85 97.7 0.088 0.124 0.088 0.992 7.4 1.9 22287 11.54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.07 99.6 0.909 0.561 0.548 1.5 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AlphaFold2 2.02 44.85 1.35 22287 1060 99.92 0.2024 0.1999 0.2004 0.2516 0.2489 Random selection 14.4
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 19.5984 f_angle_d 0.9072 f_chiral_restr 0.0542 f_bond_d 0.0081 f_plane_restr 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2058 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing