2ERF

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z78PDB ENTRY 1Z78

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.630030% PEG1500 and 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.242.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.31α = 90
b = 40.489β = 106.99
c = 60.086γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID1.00931APS19-ID

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
11.453095.80.06839.73.8341553415529.2
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)
1.451.568.70.3762.52.32422

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation 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 REPLACEMENTTHROUGHOUTPDB ENTRY 1Z781.4522.863093130931257594.380.18630.185590.183010.21672RANDOM25.962
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.762
r_dihedral_angle_4_deg19.138
r_dihedral_angle_3_deg13.208
r_dihedral_angle_1_deg6.165
r_rigid_bond_restr5.607
r_scbond_it5.434
r_scangle_it5.186
r_sphericity_free4.395
r_sphericity_bonded3.841
r_mcangle_it2.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.762
r_dihedral_angle_4_deg19.138
r_dihedral_angle_3_deg13.208
r_dihedral_angle_1_deg6.165
r_rigid_bond_restr5.607
r_scbond_it5.434
r_scangle_it5.186
r_sphericity_free4.395
r_sphericity_bonded3.841
r_mcangle_it2.27
r_mcbond_it1.473
r_angle_refined_deg1.467
r_nbtor_refined0.309
r_symmetry_vdw_refined0.235
r_nbd_refined0.215
r_xyhbond_nbd_refined0.158
r_symmetry_hbond_refined0.144
r_chiral_restr0.096
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1609
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing