1YO8 | pdb_00001yo8

Structure of the C-terminal domain of human thrombospondin-2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	298	Tris-HCl, Sodium Acetate, PEG 4000, glycine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.50

Crystal Properties
Matthews coefficient	Solvent content
3.1	58.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.437	α = 90
b = 121.588	β = 90
c = 155.33	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		2004-02-06	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	1.2662,1.0213,1.0452,1.0210	APS	14-ID-B

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	2.6	50	93.8	0.083	18.5			49844

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	2.6	2.69	60.9		0.275	2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.6	20	26106	26106	2575	95	0.224	0.224	0.218	0.2158	0.284	0.2751	RANDOM	34.081

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]
-4.15			-1.85		6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.354
r_scangle_it	3.387
r_scbond_it	2.183
r_mcangle_it	1.928
r_angle_refined_deg	1.154
r_mcbond_it	1.047
r_symmetry_vdw_refined	0.28
r_nbd_refined	0.241
r_symmetry_hbond_refined	0.205
r_xyhbond_nbd_refined	0.154
r_metal_ion_refined	0.152
r_chiral_restr	0.09
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4844
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	125

Software

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