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Crystal structure of the WD-repeat domain of human SEC31A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold ALPHAFOLD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 30%(w/v)PEG4K,0.2M Sodium Acetat, 0.1M Tris HCL pH8.5
Crystal Properties Matthews coefficient Solvent content 2.14 42.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.18 α = 90 b = 156.75 β = 99.48 c = 85.19 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 EIGER X 16M 2020-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.4 50 94.2 0.116 0.136 0.069 7.1 3.4 49159 47.81
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 2.4 2.44 75 0.781 0.917 0.473 0.7 3
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 ALPHAFOLD 2.4 44.37 49130 986 93.7 0.19 0.189 0.237 0.2525 RANDOM 53.22
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] -18.4573 4.5569 1.4622 16.995
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.31 t_omega_torsion 3.39 t_angle_deg 1.2 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.31 t_omega_torsion 3.39 t_angle_deg 1.2 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9945 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing BUSTER refinement PDB_EXTRACT data extraction HKL-3000 data processing HKL-3000 data reduction