6JB8

Crystal structure of nanobody D3-L11 in complex with hen egg-white lysozyme


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6JB2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293.1520mM Tris-HCl, 100mM NaCl, 100mM NaNO3, 16% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0239.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.24α = 90
b = 49.48β = 93.4
c = 59.28γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702016-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000Photon FactoryAR-NW12A

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
11.6540.1793.70.0760.99711.13.526392
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.74680.3990.8482.22.8

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 REPLACEMENTTHROUGHOUT6JB21.6540.1725271110793.680.170270.168570.20691RANDOM28.663
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]
0.47-0.01-0.27-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.954
r_dihedral_angle_3_deg14.069
r_dihedral_angle_4_deg12.3
r_dihedral_angle_1_deg6.763
r_long_range_B_refined4.518
r_long_range_B_other4.399
r_scangle_other2.165
r_angle_refined_deg1.815
r_mcangle_it1.567
r_mcangle_other1.567
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.954
r_dihedral_angle_3_deg14.069
r_dihedral_angle_4_deg12.3
r_dihedral_angle_1_deg6.763
r_long_range_B_refined4.518
r_long_range_B_other4.399
r_scangle_other2.165
r_angle_refined_deg1.815
r_mcangle_it1.567
r_mcangle_other1.567
r_scbond_it1.432
r_scbond_other1.42
r_mcbond_it1.097
r_mcbond_other1.097
r_angle_other_deg1.095
r_chiral_restr0.118
r_bond_refined_d0.019
r_gen_planes_refined0.01
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 Atoms1954
Nucleic Acid Atoms
Solvent Atoms276
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing