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The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D89
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M di-Ammonium hydrogen citrate
20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.86 56.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.06 α = 90 b = 48.19 β = 97.48 c = 100.3 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 2016-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000010 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 2.2 44.82 99.8 0.123 0.134 0.998 11.15 6.6 26307 50.832
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 2.2 2.26 99.9 1.462 1.587 0.712 2.04 6.74
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 2D89 2.2 44.82 24989 1316 99.79 0.1796 0.177 0.1833 0.2298 0.2271 RANDOM 53.022
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] -1.79 -1.78 -1.14 3.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.196 r_dihedral_angle_4_deg 19.416 r_dihedral_angle_3_deg 14.821 r_dihedral_angle_1_deg 5.159 r_mcangle_it 5.044 r_mcbond_it 3.723 r_mcbond_other 3.696 r_angle_refined_deg 1.595 r_angle_other_deg 0.961 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.196 r_dihedral_angle_4_deg 19.416 r_dihedral_angle_3_deg 14.821 r_dihedral_angle_1_deg 5.159 r_mcangle_it 5.044 r_mcbond_it 3.723 r_mcbond_other 3.696 r_angle_refined_deg 1.595 r_angle_other_deg 0.961 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3190 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing