7Z1D

Nanobody H11-H6 bound to RBD


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M HEPES, pH 7.5 and 20% w/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.1843.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.41α = 90
b = 65.08β = 90
c = 82.9γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.5545.0498.50.0830.99918.313.548875
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)
11.551.5997.11.2430.7462.213.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6ZBP1.5545.0448825235998.2710.1680.16670.186221.494
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]
-0.5870.1930.395
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.213
r_dihedral_angle_4_deg14.261
r_dihedral_angle_1_deg13.735
r_dihedral_angle_3_deg11.952
r_lrange_it6.441
r_lrange_other6.44
r_dihedral_angle_other_3_deg5.575
r_scangle_it5.125
r_scangle_other5.124
r_scbond_it3.398
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.213
r_dihedral_angle_4_deg14.261
r_dihedral_angle_1_deg13.735
r_dihedral_angle_3_deg11.952
r_lrange_it6.441
r_lrange_other6.44
r_dihedral_angle_other_3_deg5.575
r_scangle_it5.125
r_scangle_other5.124
r_scbond_it3.398
r_scbond_other3.397
r_mcangle_other2.955
r_mcangle_it2.949
r_mcbond_it2.038
r_mcbond_other2.022
r_angle_other_deg1.357
r_angle_refined_deg1.315
r_nbd_other0.243
r_symmetry_xyhbond_nbd_refined0.234
r_symmetry_nbd_refined0.208
r_nbd_refined0.189
r_symmetry_nbd_other0.179
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.137
r_symmetry_nbtor_other0.078
r_chiral_restr0.066
r_xyhbond_nbd_other0.028
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2525
Nucleic Acid Atoms
Solvent Atoms312
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing