X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7A91RBD
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2880.15 M DL-Malic acid pH 7.0, 0.1 M Imidazole pH 7.0, 22% PEG MME 550
Crystal Properties
Matthews coefficientSolvent content
4.6473.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.64α = 90
b = 194.24β = 90
c = 264.37γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2023-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17UM0.9792SSRFBL17UM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
13.78099.10.2050.2280.9966.6534890
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.73.82.8283.1620.321

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 REPLACEMENTTHROUGHOUT7A91, AlphaFold3.774.133025179298.870.210560.207430.26888RANDOM192.144
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]
9.97-10.70.74
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined57.977
r_long_range_B_other57.977
r_scangle_other53.716
r_mcangle_it50.998
r_mcangle_other50.995
r_scbond_it40.594
r_scbond_other40.593
r_mcbond_it38.199
r_mcbond_other38.193
r_dihedral_angle_3_deg20.112
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined57.977
r_long_range_B_other57.977
r_scangle_other53.716
r_mcangle_it50.998
r_mcangle_other50.995
r_scbond_it40.594
r_scbond_other40.593
r_mcbond_it38.199
r_mcbond_other38.193
r_dihedral_angle_3_deg20.112
r_dihedral_angle_2_deg18.355
r_dihedral_angle_1_deg15.709
r_angle_refined_deg3.344
r_angle_other_deg1.365
r_chiral_restr0.12
r_bond_refined_d0.018
r_gen_planes_refined0.016
r_bond_other_d0.006
r_gen_planes_other0.006
r_dihedral_angle_4_deg
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12286
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing