Experiment: 1Z78

Crystal Structure of the Thrombospondin-1 N-terminal domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZA4	NTSP-1 structure from NTSP-1/Arixtra complex to be deposited

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	30% PEG1500 and 0.1 M NaAc, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.812	α = 90
b = 41.899	β = 100.649
c = 53.458	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	ADSC QUANTUM 4		2004-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.07218	APS	19-ID

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	1.8	50	99.6	0.068	32.12	6.9		17415			22.74

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)
	1.8	1.86	96.8		0.427	2.75	3.1	1672

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	NTSP-1 structure from NTSP-1/Arixtra complex to be deposited	1.8	30	3	17415	14668	1472	84.23	0.253	0.237	0.236	0.2518	0.259	0.2691	Random	26.91

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]

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	26.92
c_angle_deg	1.63
c_improper_angle_d	1.39
c_bond_d	0.0066

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1594
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
AMoRE	phasing
CNS	refinement
HKL-2000	data scaling