3OSH

Crystal Structure of The Complex of Group 1 Phospholipase A2 With Atropin At 1.5 A Resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NJU 

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
2.2344.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.377α = 90
b = 42.377β = 90
c = 65.17γ = 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
11.542.4970.05873.6180661806623.6
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)
1.51.53910.5762.4

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3NJU1.542.37180661713992596.870.200780.19920.22945RANDOM22.528
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]
-0.09-0.090.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.648
r_dihedral_angle_1_deg4.341
r_scangle_it3.657
r_scbond_it2.279
r_angle_refined_deg2.174
r_mcangle_it1.628
r_angle_other_deg1.221
r_mcbond_it0.831
r_nbd_refined0.287
r_symmetry_vdw_refined0.261
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.648
r_dihedral_angle_1_deg4.341
r_scangle_it3.657
r_scbond_it2.279
r_angle_refined_deg2.174
r_mcangle_it1.628
r_angle_other_deg1.221
r_mcbond_it0.831
r_nbd_refined0.287
r_symmetry_vdw_refined0.261
r_chiral_restr0.251
r_symmetry_hbond_refined0.237
r_symmetry_vdw_other0.219
r_metal_ion_refined0.215
r_nbd_other0.201
r_xyhbond_nbd_refined0.154
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_gen_planes_other0.009
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms910
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms22

Software

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