4KF3

Crystal Structure of Myotoxin II (MjTX-II), a myotoxic Lys49-phospholipase A2 from Bothrops moojeni.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XXSPDB ENTRY 1XXS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629120% (v/v) 2-propanol, 20% (w/v) polyethylene Glycol 4000 and 0.1 M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.448.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.999α = 90
b = 62.169β = 90
c = 86.007γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2012-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.42LNLSW01B-MX2

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
11.925092.40.04410.373.919571-324.6
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)
11.921.9997.60.412.013.7

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 1XXS1.9238.96194911949194592.40.2270.2270.2270.257Random56.13
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]
-4.9-5.4510.35
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.9
c_angle_deg2.1
c_improper_angle_d0.76
c_angle_d0.03
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1873
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms120

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling