2ERF | pdb_00002erf

Crystal Structure of the Thrombospondin-1 N-terminal Domain at 1.45A Resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Z78	PDB ENTRY 1Z78

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	300	30% PEG1500 and 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.2	42.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.31	α = 90
b = 40.489	β = 106.99
c = 60.086	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 315		2005-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.00931	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	1.45	30	95.8	0.068	39.7	3.8	34155	34155			29.2

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)
	1.45	1.5	68.7		0.376	2.5	2.3	2422

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1Z78	1.45	22.86	30931	30931	2575	94.38	0.1863	0.18559	0.18301	0.18	0.21672	0.18	RANDOM	25.962

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]
-0.01			0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.762
r_dihedral_angle_4_deg	19.138
r_dihedral_angle_3_deg	13.208
r_dihedral_angle_1_deg	6.165
r_rigid_bond_restr	5.607
r_scbond_it	5.434
r_scangle_it	5.186
r_sphericity_free	4.395
r_sphericity_bonded	3.841
r_mcangle_it	2.27
r_mcbond_it	1.473
r_angle_refined_deg	1.467
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.158
r_symmetry_hbond_refined	0.144
r_chiral_restr	0.096
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1609
Nucleic Acid Atoms
Solvent Atoms	217
Heterogen Atoms

Software

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