3NJU

Crystal structure of the complex of group I phospholipase A2 with 4-Methoxy-benzoicacid at 1.4A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629310MM sodium phosphate buffer, 2M calcium chloride, 35% ethanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1743.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.074α = 90
b = 42.074β = 90
c = 64.253γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMirror2010-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

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
11.44296.50.06379.9220952209519.1
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)
11.41.42950.4485.5

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 REPLACEMENTTHROUGHOUT1OXR1.419.092209520236110296.590.177420.176730.174240.22388RANDOM25.03
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]
-0.21-0.210.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.654
r_dihedral_angle_3_deg13.516
r_dihedral_angle_4_deg10.31
r_sphericity_free7.819
r_sphericity_bonded6.052
r_dihedral_angle_1_deg5.855
r_scangle_it4.602
r_mcangle_it3.976
r_scbond_it3.645
r_mcbond_it3.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.654
r_dihedral_angle_3_deg13.516
r_dihedral_angle_4_deg10.31
r_sphericity_free7.819
r_sphericity_bonded6.052
r_dihedral_angle_1_deg5.855
r_scangle_it4.602
r_mcangle_it3.976
r_scbond_it3.645
r_mcbond_it3.101
r_rigid_bond_restr2.807
r_angle_refined_deg1.693
r_nbtor_refined0.321
r_symmetry_vdw_refined0.318
r_symmetry_hbond_refined0.278
r_nbd_refined0.262
r_xyhbond_nbd_refined0.24
r_chiral_restr0.112
r_metal_ion_refined0.08
r_bond_refined_d0.017
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms910
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms12

Software

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