1JQ8 | pdb_00001jq8

Design of specific inhibitors of phospholipase A2: Crystal structure of a complex formed between phospholipase A2 from Daboia russelli pulchella and a designed pentapeptide Leu-Ala-Ile-Tyr-Ser at 2.0 resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FE7PDB: 1FE7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529820mM Sodium cacodylate, 1.4M Ammonium sulfate, 4mM Calcium chloride, 3% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5952.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.825α = 90
b = 90.375β = 90
c = 77.59γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray180IMAGE PLATEMARRESEARCH1999-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.98EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
122096.30.0760.029.222.7179141791431.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0790.34.30.179.42.11605

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-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB: 1FE7211.94178411784186196.60.1890.1870.1870.20.1980.24RANDOM38.7
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]
0.49-1.130.64
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.3
c_scangle_it4.77
c_scbond_it3.54
c_mcangle_it3.16
c_improper_angle_d2.71
c_angle_deg2.2
c_mcbond_it2.08
c_bond_d0.032
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.3
c_scangle_it4.77
c_scbond_it3.54
c_mcangle_it3.16
c_improper_angle_d2.71
c_angle_deg2.2
c_mcbond_it2.08
c_bond_d0.032
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1928
Nucleic Acid Atoms
Solvent Atoms283
Heterogen Atoms17

Software

Software
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement