2PF5 | pdb_00002pf5

Crystal Structure of the Human TSG-6 Link Module

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UUH	1UUH - crystal structure of CD44

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	A 2.5 ul drop formed from equal amounts of protein solution (7 mg/ml solution in approximately 25mM TrisHCl and 75mM NaCl) and well solution was equilibrated against 1 ml well solution (2 M Ammonium Sulphate, 2 % v/v PEG 400 and 0.1M Sodium Hepes (pH 7.5)), VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.12	70.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.816	α = 90
b = 75.87	β = 103.42
c = 90.674	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	ADSC QUANTUM 4		2005-08-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

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	1.9	88.04	99.14	0.071	6.35	4.08		69439

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)
	1.9	2	98.62		0.41	1.51	3.98

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	1UUH - crystal structure of CD44	1.9	88.04	65938	3499	98.96	0.19596	0.19439	0.22	0.22588	0.25	RANDOM	21.78

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]
-0.19		0.66	0.3		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.67
r_dihedral_angle_4_deg	17.585
r_dihedral_angle_1_deg	14.882
r_dihedral_angle_3_deg	14.615
r_scangle_it	2.874
r_scbond_it	2.086
r_angle_refined_deg	1.66
r_mcangle_it	1.273
r_mcbond_it	0.874
r_nbtor_refined	0.311
r_symmetry_hbond_refined	0.241
r_symmetry_vdw_refined	0.221
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.118
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
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	3743
Nucleic Acid Atoms
Solvent Atoms	414
Heterogen Atoms	191

Software

Software
Software Name	Purpose
DNA	data collection
DM	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
DM	phasing