5C0N

Development of a monoclonal antibody targeting secreted aP2 to treat diabetes and fatty liver disease


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2960.1M Hepes pH 7.5, 0.2M NH2SO4, 16% PEG 4K and 10% isopropanol
Crystal Properties
Matthews coefficientSolvent content
2.5551.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.27α = 90
b = 101.95β = 90.03
c = 95.32γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77PIXELDECTRIS PILATUS 6M-F2013-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

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
12.9554.9799.20.188.36.1626312
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.953.093489

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1LIE354.9722426246698.870.194250.186360.26464RANDOM60.654
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]
-0.25-5.01-3.513.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.525
r_dihedral_angle_3_deg20.143
r_dihedral_angle_4_deg19.135
r_long_range_B_refined10.832
r_long_range_B_other10.832
r_mcangle_it7.644
r_mcangle_other7.643
r_scangle_other7.33
r_dihedral_angle_1_deg7.31
r_mcbond_it4.843
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.525
r_dihedral_angle_3_deg20.143
r_dihedral_angle_4_deg19.135
r_long_range_B_refined10.832
r_long_range_B_other10.832
r_mcangle_it7.644
r_mcangle_other7.643
r_scangle_other7.33
r_dihedral_angle_1_deg7.31
r_mcbond_it4.843
r_mcbond_other4.842
r_scbond_it4.663
r_scbond_other4.663
r_angle_refined_deg1.622
r_angle_other_deg1.085
r_chiral_restr0.085
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.004
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8541
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
SCALAdata scaling
PHASERphasing