1MF4

Structure-based design of potent and selective inhibitors of phospholipase A2: Crystal structure of the complex formed between phosholipase A2 from Naja Naja sagittifera and a designed peptide inhibitor at 1.9 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16295sodium phosphate, CaCl2, ethanol; Co-crystallation of protein: peptide in 1:10 molar ratio, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 6.00
Crystal Properties
Matthews coefficientSolvent content
2.2645.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.779α = 90
b = 42.779β = 90
c = 65.866γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray290IMAGE PLATEMARRESEARCHMONOCHROMATOR2001-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
11.92093.20.07319.31.048247-320.63
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)
11.91.9761.30.2891.9

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1LN81.919.54824782474111000.1840.1820.239RANDOM25.5
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]
-0.24-0.240.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.004
r_dihedral_angle_3_deg17.004
r_scangle_it3.903
r_dihedral_angle_1_deg3.468
r_scbond_it2.472
r_mcangle_it1.769
r_angle_refined_deg1.748
r_mcbond_it0.88
r_symmetry_hbond_refined0.689
r_symmetry_vdw_refined0.449
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.004
r_dihedral_angle_3_deg17.004
r_scangle_it3.903
r_dihedral_angle_1_deg3.468
r_scbond_it2.472
r_mcangle_it1.769
r_angle_refined_deg1.748
r_mcbond_it0.88
r_symmetry_hbond_refined0.689
r_symmetry_vdw_refined0.449
r_nbd_refined0.292
r_xyhbond_nbd_refined0.167
r_chiral_restr0.109
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms950
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms1

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement