1TK4

Crystal structure of russells viper phospholipase A2 in complex with a specifically designed tetrapeptide Ala-Ile-Arg-Ser at 1.1 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SKGPDB entry 1SKG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72980.2M AMMONIUM SULPHATE, 30% PEG , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.512α = 90
b = 52.512β = 90
c = 48.088γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMARRESEARCHmirror2004-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.806EMBL/DESY, HAMBURGX11

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
11.1501000.04122.99.7529955299510.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.11.121000.3813.52642

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 1SKG1.137.01524295291000.168440.168260.18532RANDOM13.854
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]
0.130.13-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.83
r_scangle_it2.738
r_sphericity_free2.517
r_sphericity_bonded2.403
r_scbond_it1.808
r_mcangle_it1.645
r_angle_refined_deg1.519
r_mcbond_it1.008
r_rigid_bond_restr0.939
r_angle_other_deg0.774
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.83
r_scangle_it2.738
r_sphericity_free2.517
r_sphericity_bonded2.403
r_scbond_it1.808
r_mcangle_it1.645
r_angle_refined_deg1.519
r_mcbond_it1.008
r_rigid_bond_restr0.939
r_angle_other_deg0.774
r_nbd_refined0.425
r_nbd_other0.241
r_symmetry_vdw_refined0.238
r_symmetry_vdw_other0.225
r_xyhbond_nbd_refined0.175
r_symmetry_hbond_refined0.174
r_nbtor_other0.086
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_other0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms993
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing