1TG4

Design of specific inhibitors of groupII phospholipase A2(PLA2): Crystal structure of the complex formed between russells viper PLA2 and designed peptide Phe-Leu-Ala-Tyr-Lys at 1.7A 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
2.449.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.082α = 90
b = 52.082β = 90
c = 47.784γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMARRESEARCHMIRROR2004-04-25MSINGLE 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
11.75299.70.04116.412.31420317.7
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)
1.71.7399.60.1774.4704

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 1SKG1.751.99142031346071299.80.16990.168870.167460.19603RANDOM19.149
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]
0.10.1-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.402
r_scangle_it4.47
r_dihedral_angle_1_deg3.919
r_scbond_it2.886
r_mcangle_it2.188
r_angle_refined_deg2.18
r_angle_other_deg1.287
r_mcbond_it1.211
r_nbd_refined0.434
r_symmetry_vdw_refined0.384
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.402
r_scangle_it4.47
r_dihedral_angle_1_deg3.919
r_scbond_it2.886
r_mcangle_it2.188
r_angle_refined_deg2.18
r_angle_other_deg1.287
r_mcbond_it1.211
r_nbd_refined0.434
r_symmetry_vdw_refined0.384
r_symmetry_vdw_other0.38
r_nbd_other0.254
r_xyhbond_nbd_refined0.232
r_symmetry_hbond_refined0.22
r_chiral_restr0.183
r_xyhbond_nbd_other0.073
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_gen_planes_other0.006
r_bond_other_d0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms990
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing