2I3Y

Crystal structure of human glutathione peroxidase 5

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	20% PEG 3350, 0.2 M sodium formate, 5% ETHYLENE GLYCOL, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.544	α = 90
b = 104.544	β = 90
c = 71.663	γ = 120

Symmetry
Space Group	P 62 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		2006-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.8983	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	50	99.9	0.064	23	10.6	16114	16114			27

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	2	2.11	100		0.417	5.7	10.7	2305

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 (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	pdb entry 2F8A	2	50	15269	15269	822	99.81	0.17718	0.17466	0.18	0.22835	0.23	RANDOM	37.321

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]
-2.7	-1.35		-2.7		4.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.763
r_dihedral_angle_3_deg	14.499
r_dihedral_angle_4_deg	8.149
r_dihedral_angle_1_deg	7.087
r_scangle_it	6.61
r_scbond_it	5.325
r_mcangle_it	3.558
r_mcbond_it	2.832
r_angle_refined_deg	1.458
r_angle_other_deg	0.923
r_mcbond_other	0.786
r_symmetry_vdw_other	0.319
r_nbd_other	0.197
r_nbd_refined	0.192
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.162
r_symmetry_hbond_refined	0.161
r_symmetry_vdw_refined	0.157
r_nbtor_other	0.09
r_chiral_restr	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
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	1474
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing