2PYC | pdb_00002pyc

Crystal structure of a monomeric phospholipase A2 from Russell's viper at 1.5A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SV3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6298Sodium acetate, PEG 4000, Acetonitrile, Ammonium sulphate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4149.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.442α = 90
b = 52.442β = 90
c = 47.876γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATEMAR scanner 345 mm plateMirror2007-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X310.8EMBL/DESY, HAMBURGX31

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.552.799.90.0592097319871
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.55100

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 (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1SV31.537.082097319871107599.880.182210.180450.190.21620.22RANDOM23.884
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]
0.40.4-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.844
r_dihedral_angle_1_deg4.537
r_scangle_it2.885
r_scbond_it1.817
r_angle_refined_deg1.489
r_mcangle_it1.362
r_mcbond_it0.715
r_nbd_refined0.348
r_symmetry_vdw_refined0.192
r_xyhbond_nbd_refined0.165
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms943
Nucleic Acid Atoms
Solvent Atoms285
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing