1SV3

Structure of the complex formed between Phospholipase A2 and 4-methoxybenzoic acid at 1.3A resolution.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FB2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82970.2M Ammonium sulphate, 50% PEG, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.57α = 90
b = 52.57β = 90
c = 47.823γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray203CCDMARRESEARCHMIRROR2003-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X31EMBL/DESY, HAMBURGX31

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
11.32094.10.1198.88.7287712877119.4
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)
1.31.3699.40.422.1

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 REPLACEMENTTHROUGHOUT1FB21.35202877125474136493.280.21470.209860.208220.24267RANDOM20.353
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]
0.340.34-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.632
r_dihedral_angle_1_deg3.417
r_scangle_it3.112
r_scbond_it2.15
r_angle_refined_deg1.781
r_mcangle_it1.771
r_mcbond_it1.032
r_angle_other_deg0.906
r_nbd_refined0.438
r_symmetry_hbond_refined0.243
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.632
r_dihedral_angle_1_deg3.417
r_scangle_it3.112
r_scbond_it2.15
r_angle_refined_deg1.781
r_mcangle_it1.771
r_mcbond_it1.032
r_angle_other_deg0.906
r_nbd_refined0.438
r_symmetry_hbond_refined0.243
r_nbd_other0.21
r_symmetry_vdw_refined0.196
r_xyhbond_nbd_refined0.177
r_symmetry_vdw_other0.176
r_xyhbond_nbd_other0.156
r_chiral_restr0.096
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_gen_planes_other0.005
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms944
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing