1U4J

Crystal structure of a carbohydrate induced dimer of group I phospholipase A2 from Bungarus caeruleus at 2.1 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FE5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.528150mM Tris. HCl, 2.8M NaCl, 1mM NaN3, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
2.244.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.36α = 90
b = 80.36β = 90
c = 99.44γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray180CCDMARRESEARCHmirror2004-05-06MSINGLE 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 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
12.114.399.60.1266.47.8125411247524.7
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)
2.182.3299.20.242.1

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 REPLACEMENTTHROUGHOUT1FE52.1814.26125411239763199.60.2020.1940.1940.22RANDOM24.8
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]
0.161.770.16-0.32
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.8
c_angle_deg1.6
c_improper_angle_d1.27
c_bond_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1796
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms28

Software

Software
Software NamePurpose
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing