7Z1E

Nanobody H11-H4 Q98R H100E 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 DROP2930.2M Ammonium nitrate, 20 % Peg 3350
Crystal Properties
Matthews coefficientSolvent content
2.8957.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.243α = 90
b = 78.243β = 90
c = 126.812γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-07-14MSINGLE 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
11.5967.7611000.0460.99924.918.861104
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)
11.591.621004.1560.3610.420.2

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 REPLACEMENTTHROUGHOUT6ZBP1.5967.76161035309599.9720.1630.1610.202338.799
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]
-0.473-0.237-0.4731.535
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.597
r_dihedral_angle_4_deg15.032
r_dihedral_angle_3_deg11.691
r_dihedral_angle_1_deg6.994
r_lrange_other4.131
r_lrange_it4.128
r_scangle_it3.287
r_scangle_other3.237
r_mcangle_other3.055
r_mcangle_it3.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.597
r_dihedral_angle_4_deg15.032
r_dihedral_angle_3_deg11.691
r_dihedral_angle_1_deg6.994
r_lrange_other4.131
r_lrange_it4.128
r_scangle_it3.287
r_scangle_other3.237
r_mcangle_other3.055
r_mcangle_it3.05
r_scbond_it2.621
r_scbond_other2.527
r_mcbond_it2.307
r_mcbond_other2.293
r_rigid_bond_restr1.36
r_angle_refined_deg1.306
r_angle_other_deg1.267
r_symmetry_nbd_refined0.266
r_nbd_other0.215
r_nbd_refined0.186
r_symmetry_nbd_other0.178
r_nbtor_refined0.171
r_symmetry_xyhbond_nbd_refined0.147
r_xyhbond_nbd_refined0.123
r_symmetry_nbtor_other0.075
r_chiral_restr0.061
r_bond_refined_d0.005
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 Atoms2520
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing