☰ Navigation Tabs
Structure of human Mical1 bMERB_V978A_V985A domain:Rab10 complex.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LPN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.17 M Sodium acetate, 0.085 M Tris-HCl pH 8.5, 25.5% (w/v) PEG 4000 and 15% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.66 53.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.39 α = 90 b = 48.56 β = 97.98 c = 78.77 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2021-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.999968 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.8 41.22 99.5 0.051 0.055 0.999 17.93 6.9 37165
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 0.727 0.791 0.925 1.85
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 1.8 41.22 1.36 37089 1854 99.37 0.1946 0.1928 0.1969 0.2312 0.2319
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 6.072 f_angle_d 0.828 f_chiral_restr 0.046 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2562 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing