6HKQ

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	Reservoir 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 coefficient	Solvent content
1.87	34.24

Crystal Data

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

Symmetry
Space Group	P 21 21 21

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 200K		2018-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.54	46.81	86.6	0.1	0.11	0.03	20.2	10.5		20009

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)	Redundancy	Number Unique Reflections (All)
1	1.54	1.59	72.1		0.9	0.97	0.33	0.81	2.4	6.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.54	46.81	19002	951	86.15	0.15116	0.1495	0.18416	RANDOM	18.524

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			-0.13		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.876
r_dihedral_angle_4_deg	14.775
r_dihedral_angle_3_deg	11.917
r_long_range_B_refined	7.312
r_long_range_B_other	7.143
r_dihedral_angle_1_deg	6.091
r_scangle_other	4.496
r_scbond_it	3.129
r_scbond_other	3.127
r_mcangle_other	2.631
r_mcangle_it	2.618
r_angle_refined_deg	1.701
r_mcbond_it	1.667
r_mcbond_other	1.619
r_angle_other_deg	1.023
r_chiral_restr	0.11
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
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 Atoms	Number
Protein Atoms	1339
Nucleic Acid Atoms
Solvent Atoms	228
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing