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Structure of the human TMED1 (p24gamma1) Golgi dynamics Domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GU5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 294 0.1 M sodium acetate trihydrate pH 4.6, 8% (w/v) PEG 4,000
Crystal Properties Matthews coefficient Solvent content 2.11 41.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.89 α = 90 b = 151.89 β = 90 c = 56.17 γ = 120
Symmetry Space Group P 6 2 2
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 EIGER X 16M 2020-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.72 45.16 99.9 1 19.76 39.64 41068
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.82 99.5 0.49 0.98 39.69
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 5GU5 1.72 45.16 39014 2054 99.9 0.1957 0.1944 0.2216 0.2099 RANDOM 36.356
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] -0.07 -0.04 -0.07 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.684 r_dihedral_angle_4_deg 20.4 r_dihedral_angle_3_deg 12.386 r_dihedral_angle_1_deg 7.162 r_angle_refined_deg 1.411 r_angle_other_deg 1.284 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.684 r_dihedral_angle_4_deg 20.4 r_dihedral_angle_3_deg 12.386 r_dihedral_angle_1_deg 7.162 r_angle_refined_deg 1.411 r_angle_other_deg 1.284 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2276 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing