1KQU

Human phospholipase A2 complexed with a substrate anologue


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PODPDB ENTRY 1POD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.8293sodium Chloride, Calcium Chloride, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.8356.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.55α = 90
b = 76.55β = 90
c = 93.46γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATERIGAKU RAXIS IICYALE MIRRORS1999-01-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.15093.80.09119.35.939371921820.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.1892.50.3463.18898

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1POD2.189218921895594.80.2090.2090.24RANDOM33.4
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]
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d23.1
x_scangle_it3.37
x_mcangle_it2.29
x_scbond_it2.23
x_mcbond_it1.36
x_angle_deg1.2
x_improper_angle_d1.01
x_bond_d0.006
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d23.1
x_scangle_it3.37
x_mcangle_it2.29
x_scbond_it2.23
x_mcbond_it1.36
x_angle_deg1.2
x_improper_angle_d1.01
x_bond_d0.006
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms959
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms31

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing