2QHE

Crystal structure of Ser49-PLA2 (ecarpholin S) from Echis carinatus sochureki snake venom


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JIAPDB ENTRY 1JIA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION5.629320% PEG3350, 20% iso-propanol, 0.1M sodium citrate pH5.6, EVAPORATION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.6826.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.231α = 90
b = 39.487β = 90
c = 68.942γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2006-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
125095.70.05130.856463
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)
22.0787.40.144.7575

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 1JIA220110632261194.30.1920.25530.548
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]
0.038-0.1080.069
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it2.724
c_scbond_it1.944
c_mcangle_it1.715
c_angle_deg1.258
c_mcbond_it1.199
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms959
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
MOLREPphasing