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Structure of the human RAB38 in complex with GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OEC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 20 % PEG3350, 10 % ethylene glycol, 0.1 M Bis-Tris-propane pH6 .5, 0.2 M sodium bromide
Crystal Properties Matthews coefficient Solvent content 2.11 41.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.804 α = 90 b = 144.174 β = 90 c = 77.523 γ = 90
Symmetry Space Group C 2 2 21
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 X 16M 2019-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97624 Diamond I03
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 38.76 100 0.13 0.135 0.037 0.998 12.2 13.1 14044
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 2.05 100 0.649 0.675 0.185 0.951 13.1
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 5OEC 2 38.76 13318 697 99.92 0.1656 0.1633 0.1738 0.2094 0.2186 RANDOM 28.47
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] -1.63 2.96 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.598 r_dihedral_angle_4_deg 22.225 r_dihedral_angle_3_deg 16.321 r_dihedral_angle_1_deg 7.759 r_angle_refined_deg 1.565 r_angle_other_deg 1.315 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.598 r_dihedral_angle_4_deg 22.225 r_dihedral_angle_3_deg 16.321 r_dihedral_angle_1_deg 7.759 r_angle_refined_deg 1.565 r_angle_other_deg 1.315 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1398 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction DIALS data reduction PHASER phasing