2OLI

Crystal structure of the complex formed between a group II phospholipase A2 and an indole derivative at 2.2 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZR8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.2298PEG 4000, Ammonium Sulphate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5151.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.19α = 90
b = 53.19β = 90
c = 48.4γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMAR scanner 345 mm plateMirror2007-01-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54132

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.2117.995.26531652233.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.212.2982.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1ZR82.2117.9652236395.40.1820.1770.1770.186RANDOM31.4
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]
1.431.43-2.85
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.7
c_scangle_it3.09
c_mcangle_it2.38
c_scbond_it2.05
c_angle_deg1.4
c_mcbond_it1.39
c_improper_angle_d0.78
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.7
c_scangle_it3.09
c_mcangle_it2.38
c_scbond_it2.05
c_angle_deg1.4
c_mcbond_it1.39
c_improper_angle_d0.78
c_bond_d0.007
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 Atoms944
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms14

Software

Software
Software NamePurpose
CNSrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing