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Crystal Structure of the VS1-bound StARD3 Lipid-Binding Domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I9J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.5 295 0.1 M CHES pH 9.5, 0.2 M lithium sulfate, 0.3 M sodium potassium tartrate, 0.01 M DTT
Crystal Properties Matthews coefficient Solvent content 3.41 63.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.873 α = 90 b = 83.873 β = 90 c = 82.309 γ = 120
Symmetry Space Group P 31 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 100 PIXEL DECTRIS PILATUS 6M 2022-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1 ELETTRA 11.2C
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 1.753 72.893 80.1 0.113 0.117 0.032 17.4 14.5 353233 44.36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.753 1.83 0.722 0.746 0.187 9.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.088 54.46 18942 1004 93.3 0.2074 0.2053 0.2024 0.2444 0.2324 RANDOM 44.12
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] -3.8289 -3.8289 7.6577
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.9 t_omega_torsion 3.46 t_angle_deg 0.92 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.9 t_omega_torsion 3.46 t_angle_deg 0.92 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 1708 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 40
Software Software Software Name Purpose BUSTER refinement ARP/wARP model building BALBES phasing BUSTER refinement PDB_EXTRACT data extraction autoPROC data reduction