5L7X

Afamin antibody fragment, N14 Fab, L1- glycosylated, crystal form II


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IL1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5291200 nL Fab (10mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl) plus 200 nL cocktail (30% PEG 1k, 200mM Ammonium Fluoride, NH4F)
Crystal Properties
Matthews coefficientSolvent content
2.347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.491α = 90
b = 72.196β = 90
c = 88.941γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MTorroidal Mirror Si(111)2015-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.000ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.8644.4798.60.0740.9988.83.93649140
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)
11.861.9391.30.93413

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 REPLACEMENTTHROUGHOUT1IL11.8647.0634797178398.370.192080.190190.22794RANDOM39.381
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]
-0.280.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.021
r_dihedral_angle_4_deg18.653
r_dihedral_angle_3_deg14.261
r_long_range_B_refined6.854
r_long_range_B_other6.852
r_dihedral_angle_1_deg6.772
r_scangle_other3.577
r_scbond_it2.421
r_scbond_other2.392
r_mcangle_other2.263
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.021
r_dihedral_angle_4_deg18.653
r_dihedral_angle_3_deg14.261
r_long_range_B_refined6.854
r_long_range_B_other6.852
r_dihedral_angle_1_deg6.772
r_scangle_other3.577
r_scbond_it2.421
r_scbond_other2.392
r_mcangle_other2.263
r_mcangle_it2.262
r_angle_refined_deg1.501
r_mcbond_it1.479
r_mcbond_other1.476
r_angle_other_deg0.9
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3224
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
Aimlessdata scaling
autoPROCdata reduction
BALBESphasing