5VF2

scFv 2D10 re-refined as a complex with trehalose replacing the original alpha-1,6-mannobiose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5I4F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277.15MES 6.5, Magnesium sulphate (1.5 M), potassium sodium tartrate tetrahydrate (0.1M).
Crystal Properties
Matthews coefficientSolvent content
2.7254.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.093α = 90
b = 81.093β = 90
c = 74.388γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray173.15CCDMARMOSAIC 225 mm CCD2014-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97856ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.5495099.439.675.541534

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5I4F1.5535.1137096410099.430.155610.152840.18039RANDOM26.12
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]
0.460.230.46-1.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.53
r_dihedral_angle_4_deg13.792
r_dihedral_angle_3_deg11.22
r_dihedral_angle_1_deg9.22
r_long_range_B_refined6.527
r_long_range_B_other6.245
r_scangle_other2.263
r_mcangle_it1.766
r_mcangle_other1.766
r_angle_refined_deg1.714
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.53
r_dihedral_angle_4_deg13.792
r_dihedral_angle_3_deg11.22
r_dihedral_angle_1_deg9.22
r_long_range_B_refined6.527
r_long_range_B_other6.245
r_scangle_other2.263
r_mcangle_it1.766
r_mcangle_other1.766
r_angle_refined_deg1.714
r_scbond_it1.449
r_scbond_other1.449
r_mcbond_it1.047
r_mcbond_other1.047
r_angle_other_deg0.954
r_chiral_restr0.104
r_bond_refined_d0.015
r_gen_planes_refined0.009
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 Atoms1818
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000refinement