6JB5

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


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 pH 8.0, 100mM NaCl, 100mM LiCl, 18 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1643.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.01α = 90
b = 49.44β = 93.79
c = 57.94γ = 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
11.5549.4499.70.0940.99610.85.136086
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)
11.551.63980.5940.7172.44.3

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 REPLACEMENTTHROUGHOUT6JB21.5549.4434988108399.610.132970.131820.16856RANDOM16.792
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]
0.630.49-0.57-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.929
r_sphericity_free21.438
r_dihedral_angle_4_deg16.316
r_dihedral_angle_3_deg12.479
r_dihedral_angle_1_deg6.271
r_sphericity_bonded6.049
r_long_range_B_refined3.081
r_long_range_B_other2.652
r_rigid_bond_restr2.452
r_scangle_other2.219
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.929
r_sphericity_free21.438
r_dihedral_angle_4_deg16.316
r_dihedral_angle_3_deg12.479
r_dihedral_angle_1_deg6.271
r_sphericity_bonded6.049
r_long_range_B_refined3.081
r_long_range_B_other2.652
r_rigid_bond_restr2.452
r_scangle_other2.219
r_scbond_it1.953
r_scbond_other1.951
r_mcangle_other1.774
r_mcangle_it1.771
r_mcbond_it1.589
r_angle_refined_deg1.577
r_mcbond_other1.575
r_angle_other_deg1.032
r_chiral_restr0.105
r_bond_refined_d0.014
r_gen_planes_refined0.008
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1955
Nucleic Acid Atoms
Solvent Atoms297
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing