1SHU

Crystal Structure of the von Willebrand factor A domain of human capillary morphogenesis protein 2: an anthrax toxin receptor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SHT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298PEG3350, magnesium chloride, bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3547.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.419α = 90
b = 57.419β = 90
c = 111.459γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F10.9186CHESSF1

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
11.528.7598.20.04533.37.1301933019316.4
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)
1.51.5590.50.1747.74.22728

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 REPLACEMENTTHROUGHOUT1SHT1.528.75286352863514921000.18810.18810.186680.21549RANDOM16.871
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]
0.440.44-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.073
r_sphericity_free4.153
r_scangle_it3.944
r_sphericity_bonded2.984
r_scbond_it2.543
r_mcangle_it2.174
r_rigid_bond_restr1.514
r_angle_refined_deg1.465
r_mcbond_it1.378
r_angle_other_deg0.846
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.073
r_sphericity_free4.153
r_scangle_it3.944
r_sphericity_bonded2.984
r_scbond_it2.543
r_mcangle_it2.174
r_rigid_bond_restr1.514
r_angle_refined_deg1.465
r_mcbond_it1.378
r_angle_other_deg0.846
r_symmetry_vdw_other0.349
r_nbd_other0.244
r_nbd_refined0.207
r_symmetry_vdw_refined0.19
r_symmetry_hbond_refined0.145
r_xyhbond_nbd_refined0.123
r_chiral_restr0.086
r_nbtor_other0.079
r_gen_planes_other0.015
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1396
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms1

Software

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