5IVN

BC2 nanobody in complex with the BC2 peptide tag


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293MES/imidazole, 2-Methyl-2,4-pentanediol, PEG 1000, PEG 3350, DL-Glutamatic acid monohydrate, DL-Alanine, Glycine, DL-Lysine monohydrochloride, DL-Serine
Crystal Properties
Matthews coefficientSolvent content
1.7630.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.01α = 90
b = 31.53β = 107.54
c = 35.88γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918409BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1150.5599.6118.429.561121
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
111.03

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 REPLACEMENTTHROUGHOUT5IVO150.5558063305899.690.129080.1280.14961RANDOM11.701
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]
0.46-0.480.17-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free68.402
r_dihedral_angle_2_deg31.053
r_dihedral_angle_4_deg20.613
r_sphericity_bonded15.871
r_dihedral_angle_3_deg13.094
r_long_range_B_refined7.266
r_rigid_bond_restr7.261
r_dihedral_angle_1_deg7.182
r_long_range_B_other7.086
r_mcangle_it6.645
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free68.402
r_dihedral_angle_2_deg31.053
r_dihedral_angle_4_deg20.613
r_sphericity_bonded15.871
r_dihedral_angle_3_deg13.094
r_long_range_B_refined7.266
r_rigid_bond_restr7.261
r_dihedral_angle_1_deg7.182
r_long_range_B_other7.086
r_mcangle_it6.645
r_mcangle_other6.64
r_mcbond_other5.343
r_mcbond_it5.338
r_scangle_other5.299
r_scbond_it4.747
r_scbond_other4.743
r_angle_refined_deg1.549
r_angle_other_deg1.095
r_chiral_restr0.119
r_bond_refined_d0.022
r_gen_planes_refined0.013
r_gen_planes_other0.006
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1042
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing