5LZ9

Fragment-based inhibitors of Lipoprotein associated Phospholipase A2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.42930.1M HEPES/NaOHpH=7.4, 1.3M NaCl, 32.0%w/v PEG 3350,
Crystal Properties
Matthews coefficientSolvent content
2.4650.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.044α = 90
b = 91.332β = 111.97
c = 51.357γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442012-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.0644.3998.60.06810.62.426409
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.062.1289.20.6471.6

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.0644.3924691132498.40.185760.183220.23296RANDOM43.51
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]
-0.051.03-1.420.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.746
r_dihedral_angle_3_deg14.402
r_dihedral_angle_4_deg12.691
r_dihedral_angle_1_deg6.17
r_long_range_B_refined3.453
r_scbond_it1.773
r_scbond_other1.772
r_mcbond_it1.459
r_mcbond_other1.459
r_angle_refined_deg1.445
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.746
r_dihedral_angle_3_deg14.402
r_dihedral_angle_4_deg12.691
r_dihedral_angle_1_deg6.17
r_long_range_B_refined3.453
r_scbond_it1.773
r_scbond_other1.772
r_mcbond_it1.459
r_mcbond_other1.459
r_angle_refined_deg1.445
r_angle_other_deg1.257
r_chiral_restr0.086
r_bond_refined_d0.01
r_bond_other_d0.002
r_gen_planes_refined0.001
r_gen_planes_other0.001
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 Atoms2971
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing