2GS3

Crystal structure of the selenocysteine to glycine mutant of human glutathione peroxidase 4(GPX4)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	293	20% PEG 3350, 0.2 M ammonium chloride, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.58	73.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.945	α = 90
b = 62.945	β = 90
c = 195.984	γ = 90

Symmetry
Space Group	P 41 21 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	CCD	MARRESEARCH		2006-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.95	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.9	50	99.9	0.096	12.9	5.7	32109	32109			33.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	100		0.415	3.5	4.7	4550

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2F8A	1.9	50	30562	30562	1487	99.88	0.17251	0.17251	0.17163	0.1908	RANDOM	33.285

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]
0.99			0.99		-1.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.715
r_dihedral_angle_4_deg	20.769
r_dihedral_angle_3_deg	13.003
r_scangle_it	8.532
r_scbond_it	6.76
r_dihedral_angle_1_deg	6.024
r_mcangle_it	4.394
r_mcbond_it	3.123
r_angle_refined_deg	1.361
r_angle_other_deg	0.891
r_mcbond_other	0.888
r_nbd_refined	0.216
r_symmetry_vdw_other	0.196
r_nbd_other	0.19
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.149
r_symmetry_vdw_refined	0.144
r_symmetry_hbond_refined	0.11
r_chiral_restr	0.086
r_nbtor_other	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1361
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing