2P31

Crystal structure of human glutathione peroxidase 7

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GS3	PDB entry 2GS3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	25% PEG 3350, 200 mM Ammoniun sulfate, 17% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.046	α = 90
b = 56.224	β = 91.27
c = 94.593	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARMOSAIC 225 mm CCD		2007-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.95370	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	32.04	100	0.144	9	3.6	22890	22890			17.8

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		0.575	1.9	3.2	3293

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	PDB entry 2GS3	2	30	21721	21721	1152	99.99	0.166	0.166	0.16338	0.17	0.2149	0.22	RANDOM	15.875

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]
0.46		-0.33	-1.79		1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.434
r_dihedral_angle_4_deg	17.586
r_dihedral_angle_3_deg	13.62
r_scangle_it	7.25
r_dihedral_angle_1_deg	6.369
r_scbond_it	5.453
r_mcangle_it	3.5
r_mcbond_it	2.812
r_angle_refined_deg	1.432
r_angle_other_deg	0.957
r_mcbond_other	0.795
r_symmetry_vdw_other	0.205
r_nbd_refined	0.196
r_nbd_other	0.189
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.155
r_symmetry_hbond_refined	0.146
r_symmetry_vdw_refined	0.116
r_chiral_restr	0.088
r_nbtor_other	0.086
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	2454
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	2

Software

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