6I3Y

Crystal structure of the human mitochondrial PRELID1K58V-TRIAP1 complex with PS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6I3V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.15100 mM sodium cacodylate pH 6.5 40% PEG 300
Crystal Properties
Matthews coefficientSolvent content
3.3262.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126α = 90
b = 126β = 90
c = 178.32γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.98631009.137.117749
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.983.03100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6I3V2.98631684487499.840.246720.243760.29892RANDOM105.079
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]
3.881.943.88-12.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.053
r_dihedral_angle_4_deg21.999
r_dihedral_angle_3_deg20.619
r_scangle_other12.714
r_mcangle_it12.384
r_mcangle_other12.384
r_scbond_it8.267
r_scbond_other8.264
r_mcbond_other8.069
r_mcbond_it8.066
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.053
r_dihedral_angle_4_deg21.999
r_dihedral_angle_3_deg20.619
r_scangle_other12.714
r_mcangle_it12.384
r_mcangle_other12.384
r_scbond_it8.267
r_scbond_other8.264
r_mcbond_other8.069
r_mcbond_it8.066
r_dihedral_angle_1_deg6.595
r_angle_refined_deg1.527
r_angle_other_deg1.16
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.003
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 AtomsNumber
Protein Atoms3817
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing