2DPZ

Structure of the complex of phospholipase A2 with N-(4-hydroxyphenyl)- acetamide at 2.1 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.82980.2M ammonium sulphate, 30% PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4950.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.063α = 90
b = 53.063β = 90
c = 48.201γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray292IMAGE PLATEMAR scanner 345 mm plate2005-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5412

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.152.798.578157815
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.1490.9

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 REPLACEMENTTHROUGHOUT1FB22.1207815743736298.50.210.205310.204720.21701RANDOM33.131
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]
0.380.38-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.68
r_scangle_it3.572
r_dihedral_angle_1_deg3.534
r_scbond_it2.171
r_angle_refined_deg1.696
r_mcangle_it1.605
r_mcbond_it0.862
r_symmetry_hbond_refined0.523
r_nbd_refined0.392
r_xyhbond_nbd_refined0.239
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.68
r_scangle_it3.572
r_dihedral_angle_1_deg3.534
r_scbond_it2.171
r_angle_refined_deg1.696
r_mcangle_it1.605
r_mcbond_it0.862
r_symmetry_hbond_refined0.523
r_nbd_refined0.392
r_xyhbond_nbd_refined0.239
r_symmetry_vdw_refined0.19
r_chiral_restr0.1
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms938
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
AUTOMARdata reduction
AMoREphasing