5JAN | pdb_00005jan

Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA<sub>2</sub>) Discovered Through X-Ray Fragment Screening


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.42971.0M NaCl, 0.1M HEPES/NaOHpH=7.4, 28.8%w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3347.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.373α = 90
b = 92.08β = 112.6
c = 48.273γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRIGAKU SATURN 944+2010-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54

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
12.1246.3399.27.53.621778

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT2.1246.3321778117299.20.225190.222910.230.266930.27RANDOM34.96
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]
-2.670.78-2.143.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.836
r_dihedral_angle_3_deg14.233
r_dihedral_angle_4_deg13.984
r_dihedral_angle_1_deg6.805
r_long_range_B_refined3.396
r_angle_refined_deg1.425
r_scbond_it1.347
r_scbond_other1.347
r_mcbond_it1.057
r_mcbond_other1.036
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.836
r_dihedral_angle_3_deg14.233
r_dihedral_angle_4_deg13.984
r_dihedral_angle_1_deg6.805
r_long_range_B_refined3.396
r_angle_refined_deg1.425
r_scbond_it1.347
r_scbond_other1.347
r_mcbond_it1.057
r_mcbond_other1.036
r_angle_other_deg0.932
r_chiral_restr0.082
r_bond_refined_d0.011
r_bond_other_d0.002
r_gen_planes_refined
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_it
r_mcangle_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2978
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
SCALAdata scaling