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Structure of the human RAB3C in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZBD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 25% PEG3350, 0.1M BIS-TRIS pH 6.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.19 α = 86.02 b = 40.434 β = 74.16 c = 66.362 γ = 66.45
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER2 XE 16M 2019-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
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 2.3 63.78 98.4 0.08 0.094 0.049 0.997 9.5 3.6 16096
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 2.3 2.38 97.8 0.573 0.672 0.349 0.789 3.6
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 1ZBD 2.3 63.78 15301 792 98.39 0.2041 0.1999 0.2048 0.2895 0.2896 RANDOM 43.127
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] -0.44 -0.31 0.15 1.66 -2.27 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.175 r_dihedral_angle_3_deg 16.064 r_dihedral_angle_4_deg 10.258 r_dihedral_angle_1_deg 7.151 r_angle_refined_deg 1.498 r_angle_other_deg 1.204 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.175 r_dihedral_angle_3_deg 16.064 r_dihedral_angle_4_deg 10.258 r_dihedral_angle_1_deg 7.151 r_angle_refined_deg 1.498 r_angle_other_deg 1.204 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2655 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction DIALS data reduction