5LZ5 | pdb_00005lz5

Fragment-based inhibitors of Lipoprotein associated Phospholipase A2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.429328.0%w/v PEG 3350, 0.1M HEPES/NaOHpH=7.4, 1.3M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.3647.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.091α = 90
b = 91.494β = 111.92
c = 48.648γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442011-06-09MSINGLE 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
12.0532.7597.70.1078.92.625783
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)
12.052.1287.90.62.3

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.0532.7523942129897.780.186370.183560.190.237910.24RANDOM31.922
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]
-1.131.13-1.411.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.654
r_dihedral_angle_3_deg14.864
r_dihedral_angle_4_deg11.19
r_dihedral_angle_1_deg6.734
r_long_range_B_refined2.408
r_angle_refined_deg1.467
r_angle_other_deg1.247
r_scbond_it1.228
r_scbond_other1.228
r_mcbond_other0.968
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2978
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing