5L9D

AFAMIN ANTIBODY FRAGMENT, N14 FAB, L1- GLYCOSYLATED, CRYSTAL FORM I, parsimonious model


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.8291200NL FAB 10MG/ML IN 20 MM HEPES PH 7.5 REMARK 280 7.5, 150 MM NACL PLUS 200NL 30%W/V PEG 1K, 200MM KF, pH 5.8)
Crystal Properties
Matthews coefficientSolvent content
2.1943.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.782α = 90
b = 69.249β = 90
c = 87.803γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MTORROIDAL FOCUSSING MIRROR2015-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.0000ESRFID29

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
11.8854.3799.40.07699.84.53424936.6
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)
11.881.9597.70.81.43.2

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 REPLACEMENTTHROUGHOUT1IL11.8847.3832346165999.140.178190.176230.21505RANDOM35.896
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]
1.75-0.56-1.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.013
r_dihedral_angle_4_deg22.747
r_dihedral_angle_3_deg12.886
r_dihedral_angle_1_deg6.53
r_long_range_B_refined6.392
r_long_range_B_other6.364
r_scangle_other4.477
r_mcangle_other3.051
r_mcangle_it3.049
r_scbond_it3.018
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.013
r_dihedral_angle_4_deg22.747
r_dihedral_angle_3_deg12.886
r_dihedral_angle_1_deg6.53
r_long_range_B_refined6.392
r_long_range_B_other6.364
r_scangle_other4.477
r_mcangle_other3.051
r_mcangle_it3.049
r_scbond_it3.018
r_scbond_other3.018
r_mcbond_it2.076
r_mcbond_other2.071
r_angle_refined_deg1.355
r_angle_other_deg0.864
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms3280
Nucleic Acid Atoms
Solvent Atoms221
Heterogen Atoms97

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
BALBESphasing