1OXL | pdb_00001oxl

INHIBITION OF PHOSPHOLIPASE A2 (PLA2) BY (2-CARBAMOYLMETHYL-5-PROPYL-OCTAHYDRO-INDOL-7-YL)-ACETIC ACID (INDOLE): CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN PLA2 FROM RUSSELL'S VIPER AND INDOLE AT 1.8 RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FB2PDB ENTRY 1FB2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72901.2 Ammonium sulphate buffer with 20mm sodium cacodylate, 50mm calcium chloride, 3% dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.02α = 90
b = 88.442β = 90
c = 78.106γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATEMARRESEARCHMirror2001-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X310.91EMBL/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
11.82090.20.03139.96.5216152161523.59
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)
1.81.8692.40.0832.1

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-Work (Depositor)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1FB21.819.21216152161511661000.190590.190590.18810.23816RANDOM24.094
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]
-0.86-0.411.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg18.185
r_dihedral_angle_1_deg3.694
r_scangle_it3.141
r_scbond_it1.948
r_angle_refined_deg1.861
r_mcangle_it1.404
r_angle_other_deg1.047
r_mcbond_it0.747
r_nbd_refined0.352
r_symmetry_hbond_refined0.239
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg18.185
r_dihedral_angle_1_deg3.694
r_scangle_it3.141
r_scbond_it1.948
r_angle_refined_deg1.861
r_mcangle_it1.404
r_angle_other_deg1.047
r_mcbond_it0.747
r_nbd_refined0.352
r_symmetry_hbond_refined0.239
r_nbd_other0.217
r_symmetry_vdw_refined0.216
r_symmetry_vdw_other0.214
r_symmetry_hbond_other0.202
r_xyhbond_nbd_refined0.186
r_chiral_restr0.085
r_xyhbond_nbd_other0.016
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbtor_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1887
Nucleic Acid Atoms
Solvent Atoms284
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing