2Q2F | pdb_00002q2f

Structure of the human Selenoprotein S (VCP-interacting membrane protein)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	Protein buffer: 100mM NaCl, 50mM Tris-HCl pH 8.0, 1mM EDTA, 2mM CaCl2, 5mM Beta-mercaptoethanol. Crystallization buffer: 13% PEG2000 MME, 0.1M Sodium acetate pH 4.6, 0.1M KSCN. Cryo: 30% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.666	α = 90
b = 18.705	β = 93.36
c = 37.992	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 300 mm CCD		2007-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97927	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.5	31.2	98.1	0.085	25.08	7	13654	13654		-3	19.86

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.55	88		0.325	4.2	5.8	1216

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	SAD	THROUGHOUT	1.5	31.2	12947	668	97.9	0.18291	0.18291	0.18135	0.1845	0.21434	0.2179	RANDOM	21.637

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]
0.43		2.12	-0.46		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.99
r_dihedral_angle_4_deg	15.702
r_dihedral_angle_3_deg	14.956
r_scangle_it	6.453
r_scbond_it	4.771
r_dihedral_angle_1_deg	3.675
r_mcangle_it	2.356
r_mcbond_it	1.856
r_angle_refined_deg	1.498
r_nbtor_refined	0.286
r_symmetry_vdw_refined	0.244
r_nbd_refined	0.217
r_symmetry_hbond_refined	0.189
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.099
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	577
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing