7OAP

Nanobody H3 AND C1 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 DROP2931.0 M Lithium chloride, 0.1 M Citrate pH 4, 20 % Peg 6000
Crystal Properties
Matthews coefficientSolvent content
2.9458.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.683α = 90
b = 105.683β = 90
c = 112.539γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9762DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
11.962.2541000.0250.9914.425.450645
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.951000.940.722.1

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 REPLACEMENTFREE R-VALUE6ZBP1.90162.25450645265699.9230.1820.18020.20444.25
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]
0.7590.759-1.518
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.989
r_dihedral_angle_4_deg14.764
r_dihedral_angle_3_deg13.46
r_dihedral_angle_1_deg7.375
r_lrange_other7.254
r_lrange_it7.253
r_scangle_it4.978
r_scangle_other4.977
r_scbond_it3.37
r_scbond_other3.194
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.989
r_dihedral_angle_4_deg14.764
r_dihedral_angle_3_deg13.46
r_dihedral_angle_1_deg7.375
r_lrange_other7.254
r_lrange_it7.253
r_scangle_it4.978
r_scangle_other4.977
r_scbond_it3.37
r_scbond_other3.194
r_mcangle_other2.938
r_mcangle_it2.937
r_mcbond_it2.04
r_mcbond_other2.036
r_angle_refined_deg1.528
r_angle_other_deg1.342
r_symmetry_nbd_refined0.235
r_nbd_other0.22
r_nbd_refined0.192
r_symmetry_nbd_other0.175
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.146
r_symmetry_xyhbond_nbd_refined0.135
r_symmetry_nbtor_other0.077
r_chiral_restr0.068
r_symmetry_xyhbond_nbd_other0.04
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3509
Nucleic Acid Atoms
Solvent Atoms235
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing