1XDT

COMPLEX OF DIPHTHERIA TOXIN AND HEPARIN-BINDING EPIDERMAL GROWTH FACTOR


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5PROTEIN (15 MG/ML) IN 10 MM TRIS-HCL (PH 7.5), 0.15 M NACL MIXED WITH AN EQUAL VOLUME OF PRECIPITANT CONTAINING 50 MM TRIS-HCL (PH 7.5), 0.15 M NACL, 5% (V/V) GLYCEROL, 22-30% (W/V) POLYETHYLENE GLYCOL 3350; AND EQUILIBRATED BY VAPOR DIFFUSION AGAINST PRECIPITANT, vapor diffusion
Crystal Properties
Matthews coefficientSolvent content
2.345

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.4α = 90
b = 103.7β = 90
c = 127.7γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMACSCIENCEMIRRORS1996-10-26M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.652588.50.0520.05227.93.654532
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.7479.20.1520.15252.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1MDT2.65251551175088.50.1720.1720.29RANDOM37.9
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
KeyRefinement Restraint Deviation
x_dihedral_angle_d24.3
x_scangle_it7.35
x_scbond_it5.23
x_mcangle_it5.21
x_mcbond_it3.45
x_angle_deg1.5
x_improper_angle_d1.34
x_bond_d0.009
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d24.3
x_scangle_it7.35
x_scbond_it5.23
x_mcangle_it5.21
x_mcbond_it3.45
x_angle_deg1.5
x_improper_angle_d1.34
x_bond_d0.009
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4306
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement