3UX7 | pdb_00003ux7

Crystal structure of a dimeric myotoxic component of the Vipera ammodytes meridionalis venom reveals determinants of myotoxicity and membrane damaging activity


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROPSingle crystals suitable for X-ray analysis were obtained after 5 days by the hanging-drop vapour-diffusion technique, using a protein solution with concentration of 10mg/ml in water. The reservoir solution contained 25.5% PEG-4000, 0.17 M ammonium sulphate and 15% glycerol., VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.1642.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.966α = 90
b = 47.673β = 90.25
c = 126.619γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8123EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.954021213

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.97401791597297.050.226260.224390.230.260790.26RANDOM27.764
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]
3.77-0.61-1.71-2.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.622
r_dihedral_angle_4_deg20.067
r_dihedral_angle_3_deg18.532
r_dihedral_angle_1_deg5.876
r_angle_refined_deg1.279
r_chiral_restr0.085
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7463
Nucleic Acid Atoms
Solvent Atoms90
Heterogen Atoms95

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling