2HE3 | pdb_00002he3

Crystal structure of the selenocysteine to cysteine mutant of human glutathionine peroxidase 2 (GPX2)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F8A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	20% PEG 3350, 200 mM sodium formate, 100 mM Bis-Tris propane, 10% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.308	α = 90
b = 117.212	β = 90
c = 120.157	γ = 90

Symmetry
Space Group	I 2 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	CCD	MARRESEARCH		2006-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9183	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	2.1	42	99.8	0.137	14.9	9.1	17619	17619			27

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	2.1	2.21	98.7		3.2	6.3	2496

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2f8a	2.1	42	16588	16588	890	99.73	0.15833	0.15833	0.15583	0.16	0.20481	0.21	RANDOM	21.278

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]
1.44			-0.91		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.269
r_dihedral_angle_3_deg	12.29
r_dihedral_angle_4_deg	10.771
r_scangle_it	8.134
r_dihedral_angle_1_deg	6.564
r_scbond_it	6.059
r_mcangle_it	3.746
r_mcbond_it	2.74
r_angle_refined_deg	1.464
r_angle_other_deg	0.958
r_mcbond_other	0.712
r_symmetry_vdw_other	0.312
r_nbd_refined	0.199
r_nbd_other	0.197
r_nbtor_refined	0.182
r_symmetry_hbond_refined	0.146
r_symmetry_vdw_refined	0.142
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.087
r_nbtor_other	0.084
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
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	1504
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing