6JB2

Crystal structure of nanobody D3-L11 mutant Y102A in complex with hen egg-white lysozyme


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293.1520mM TRIS HCl, 100mM NaCl, 100mM Sodium nitrate, 16% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1743.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.04α = 90
b = 49.4β = 93.7
c = 58.02γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702015-05-18MSINGLE 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
11.533.9797.80.0850.99611.95.339075
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)
11.51.58850.480.8042.83.9

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 REPLACEMENTTHROUGHOUT1ZVY1.533.9737892116797.730.126080.124790.16494RANDOM16.993
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]
0.660.38-0.56-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.118
r_sphericity_free25.784
r_dihedral_angle_4_deg16.869
r_dihedral_angle_3_deg12.413
r_sphericity_bonded9.124
r_dihedral_angle_1_deg6.469
r_rigid_bond_restr4.256
r_long_range_B_refined3.973
r_long_range_B_other3.748
r_scangle_other3.523
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.118
r_sphericity_free25.784
r_dihedral_angle_4_deg16.869
r_dihedral_angle_3_deg12.413
r_sphericity_bonded9.124
r_dihedral_angle_1_deg6.469
r_rigid_bond_restr4.256
r_long_range_B_refined3.973
r_long_range_B_other3.748
r_scangle_other3.523
r_scbond_other3.085
r_scbond_it3.084
r_mcangle_other2.127
r_mcangle_it2.126
r_mcbond_it2.103
r_mcbond_other2.08
r_angle_refined_deg1.575
r_angle_other_deg0.896
r_chiral_restr0.106
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1955
Nucleic Acid Atoms
Solvent Atoms293
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing