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Crystal structure of the human mitochondrial PRELID1K58V-TRIAP1 complex with PS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I3V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 100 mM sodium cacodylate pH 6.5
40% PEG 300
Crystal Properties Matthews coefficient Solvent content 3.32 62.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126 α = 90 b = 126 β = 90 c = 178.32 γ = 120
Symmetry Space Group P 63 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 PILATUS 6M-F 2018-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.98 63 100 9.1 37.1 17749
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.98 3.03 100
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 6I3V 2.98 63 16844 874 99.84 0.24672 0.24376 0.2475 0.29892 0.2939 RANDOM 105.079
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] 3.88 1.94 3.88 -12.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.053 r_dihedral_angle_4_deg 21.999 r_dihedral_angle_3_deg 20.619 r_scangle_other 12.714 r_mcangle_it 12.384 r_mcangle_other 12.384 r_scbond_it 8.267 r_scbond_other 8.264 r_mcbond_other 8.069 r_mcbond_it 8.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.053 r_dihedral_angle_4_deg 21.999 r_dihedral_angle_3_deg 20.619 r_scangle_other 12.714 r_mcangle_it 12.384 r_mcangle_other 12.384 r_scbond_it 8.267 r_scbond_other 8.264 r_mcbond_other 8.069 r_mcbond_it 8.066 r_dihedral_angle_1_deg 6.595 r_angle_refined_deg 1.527 r_angle_other_deg 1.16 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3817 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing