1TJ9 | pdb_00001tj9

Structure of the complexed formed between group II phospholipase A2 and a rationally designed tetra peptide,Val-Ala-Arg-Ser at 1.1A 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 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.513α = 90
b = 52.513β = 90
c = 48.037γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMARRESEARCHMIRROR2004-05-02MSINGLE 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
11.1521000.07122.515.3530315303111
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)
11.11.121000.5222.4

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-Work (Depositor)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1SKG1.1525303151861108899.850.1880.187070.186650.20896RANDOM13.218
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]
0.140.14-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.643
r_dihedral_angle_1_deg4.366
r_scangle_it2.548
r_scbond_it1.682
r_angle_refined_deg1.646
r_mcangle_it1.471
r_mcbond_it0.841
r_angle_other_deg0.707
r_nbd_refined0.441
r_nbd_other0.223
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.643
r_dihedral_angle_1_deg4.366
r_scangle_it2.548
r_scbond_it1.682
r_angle_refined_deg1.646
r_mcangle_it1.471
r_mcbond_it0.841
r_angle_other_deg0.707
r_nbd_refined0.441
r_nbd_other0.223
r_symmetry_vdw_refined0.219
r_symmetry_vdw_other0.211
r_xyhbond_nbd_refined0.179
r_symmetry_hbond_refined0.148
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms974
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing