7OAO

Nanobody C5 bound to RBD


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.2 M Sodium Acetate, 0.1 M Sodium Cacodylate pH 6.5, 30 % w/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.1141.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.22α = 90
b = 154.33β = 90
c = 28.82γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-07-14MSINGLE 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
11.551.44399.40.013128.111.851783
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5493.70.150.966

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-VALUE6ZBP1.551.44351782255599.3510.1540.15210.18625.667
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]
2.782-2.664-0.118
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.572
r_dihedral_angle_4_deg16.935
r_dihedral_angle_3_deg11.178
r_dihedral_angle_1_deg6.983
r_lrange_other3.21
r_lrange_it3.205
r_scangle_it2.18
r_scangle_other2.18
r_mcangle_other2.046
r_mcangle_it2.044
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.572
r_dihedral_angle_4_deg16.935
r_dihedral_angle_3_deg11.178
r_dihedral_angle_1_deg6.983
r_lrange_other3.21
r_lrange_it3.205
r_scangle_it2.18
r_scangle_other2.18
r_mcangle_other2.046
r_mcangle_it2.044
r_rigid_bond_restr1.856
r_scbond_it1.711
r_scbond_other1.711
r_mcbond_it1.579
r_mcbond_other1.57
r_angle_refined_deg1.443
r_angle_other_deg1.388
r_symmetry_nbd_refined0.26
r_symmetry_xyhbond_nbd_refined0.235
r_xyhbond_nbd_refined0.23
r_nbd_other0.23
r_nbd_refined0.197
r_symmetry_nbd_other0.176
r_nbtor_refined0.171
r_symmetry_nbtor_other0.077
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2452
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing