6HKQ

Human GPX4 in complex with covalent Inhibitor ML162 (S enantiomer)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293Reservoir made from 0.2 M ammonium sulfate, 20% (w/v) PEG 3350. Prio to crystal set-up, the protein was modified with covalent inhibitor, purified via gelfiltration and concentrated to 13.5 mg/ml in 50 mM TrisHCl pH 8.0, 150 mM NaCl, 5mM TCEP
Crystal Properties
Matthews coefficientSolvent content
1.8734.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.734α = 90
b = 57.249β = 90
c = 81.311γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2018-03-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.5446.8186.60.10.110.0320.210.520009
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.541.5972.10.90.970.330.812.46.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.5446.811900295186.150.151160.14950.18416RANDOM18.524
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]
-0.05-0.130.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.876
r_dihedral_angle_4_deg14.775
r_dihedral_angle_3_deg11.917
r_long_range_B_refined7.312
r_long_range_B_other7.143
r_dihedral_angle_1_deg6.091
r_scangle_other4.496
r_scbond_it3.129
r_scbond_other3.127
r_mcangle_other2.631
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.876
r_dihedral_angle_4_deg14.775
r_dihedral_angle_3_deg11.917
r_long_range_B_refined7.312
r_long_range_B_other7.143
r_dihedral_angle_1_deg6.091
r_scangle_other4.496
r_scbond_it3.129
r_scbond_other3.127
r_mcangle_other2.631
r_mcangle_it2.618
r_angle_refined_deg1.701
r_mcbond_it1.667
r_mcbond_other1.619
r_angle_other_deg1.023
r_chiral_restr0.11
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms1339
Nucleic Acid Atoms
Solvent Atoms228
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing