3CYN

The structure of human GPX8

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2P31	PDB entry 2p31

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	2 M ammonium sulfate, 1.5 % PEG 400, 0.1 M hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.688	α = 90
b = 120.854	β = 119.38
c = 75.603	γ = 90

Symmetry
Space Group	C 1 2 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		2008-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000	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	44.99	99.7	0.092	8.9	4.1	47649	47649			29

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	99.2		0.394	3.1	4.1	6901

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	PDB entry 2p31	2	44.99	45240	45240	2404	99.57	0.17217	0.17217	0.17073	0.1989	RANDOM	26.557

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]
0.22		0.03	0.66		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.389
r_dihedral_angle_4_deg	14.314
r_dihedral_angle_3_deg	13.106
r_dihedral_angle_1_deg	6.024
r_scangle_it	5.637
r_scbond_it	4.361
r_mcangle_it	2.636
r_mcbond_it	1.985
r_angle_refined_deg	1.217
r_angle_other_deg	0.892
r_mcbond_other	0.444
r_symmetry_vdw_other	0.236
r_nbd_refined	0.195
r_nbd_other	0.183
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.166
r_symmetry_vdw_refined	0.139
r_symmetry_hbond_refined	0.094
r_nbtor_other	0.083
r_chiral_restr	0.076
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
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	4203
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	48

Software

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