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Structure of the human RAB39B in complex with GMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A5J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 293 0.1 M HEPES pH 7.1, 19 % PEG3350
Crystal Properties Matthews coefficient Solvent content 1.98 37.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.725 α = 90 b = 35.285 β = 107.51 c = 53.605 γ = 90
Symmetry Space Group P 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 80 PIXEL DECTRIS EIGER2 X 16M 2019-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.91587 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 1.7 50.28 99.9 0.105 0.115 0.045 0.997 8.8 6.4 20997
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 1.7 1.73 99.9 0.842 0.923 0.373 0.843 1.8 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2A5J 1.7 50.28 20021 975 99.84 0.186 0.1838 0.2286 0.2339 RANDOM 23.516
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] -1.42 0.98 -0.16 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.623 r_dihedral_angle_3_deg 14.404 r_dihedral_angle_4_deg 13.989 r_dihedral_angle_1_deg 6.845 r_angle_refined_deg 1.584 r_angle_other_deg 1.434 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.623 r_dihedral_angle_3_deg 14.404 r_dihedral_angle_4_deg 13.989 r_dihedral_angle_1_deg 6.845 r_angle_refined_deg 1.584 r_angle_other_deg 1.434 r_chiral_restr 0.084 r_bond_refined_d 0.011 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 1543 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction DIALS data reduction PHASER phasing