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Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-D1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W24
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 3.5 M Sodium Formate
Crystal Properties Matthews coefficient Solvent content 2.25 45.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.39 α = 90 b = 43.77 β = 100.53 c = 43.14 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 16M 2018-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953729 Australian Synchrotron MX2
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 42.41 99.9 0.077 0.083 0.032 0.999 12.2 6.9 14169 26.373
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 2.06 98.8 0.585 0.632 0.235 0.917 2.5 7
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1W24 2.01 42.41 1.37769675716 14158 757 99.8378111558 0.192184947795 0.190256962422 0.192 0.225310601564 0.2277 32.3112114153
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 19.8464929628 f_angle_d 1.20977216899 f_chiral_restr 0.0813764045974 f_bond_d 0.00719178480832 f_plane_restr 0.00621700268059
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1590 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction