3R6B

Crystal Structure of Thrombospondin-1 TSR Domains 2 and 3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LSLPDB ENTRY 1LSL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52930.9M sodium potassium phosphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.5451.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.364α = 90
b = 84.817β = 90
c = 60.707γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRIGAKU SATURN 944+2011-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.430.354940.06516.65.86564656439.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4987.60.2274.73.84691

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 1LSL2.430.3546519651965393.320.23870.23870.23480.2729RANDOM
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]
-5.4604-3.25018.7105
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.171
f_angle_d1.286
f_chiral_restr0.088
f_bond_d0.008
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms855
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms32

Software

Software
Software NamePurpose
StructureStudiodata collection
PHENIXmodel building
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing