2IEQ

Core Structure of S2 from the Human Coronavirus NL63 Spike Glycoprotein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZV8PDB ENTRY 1ZV8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.2298PEG 400, sodium acetate, Imidazole, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.935.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.02α = 90
b = 51.688β = 107.56
c = 54.08γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2006-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4C0.9795NSLSX4C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.74751.5795.60.06810.73.2256682566820.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.7471.8198.10.3633.73.12573

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1ZV81.74751.572566825668129295.60.19860.198660.196430.23977RANDOM23.486
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]
0.430.970.030.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.82
r_dihedral_angle_3_deg14.962
r_scangle_it5.963
r_dihedral_angle_1_deg4.538
r_scbond_it3.48
r_mcangle_it2.051
r_angle_refined_deg1.502
r_mcbond_it1.145
r_nbtor_refined0.299
r_symmetry_vdw_refined0.223
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.82
r_dihedral_angle_3_deg14.962
r_scangle_it5.963
r_dihedral_angle_1_deg4.538
r_scbond_it3.48
r_mcangle_it2.051
r_angle_refined_deg1.502
r_mcbond_it1.145
r_nbtor_refined0.299
r_symmetry_vdw_refined0.223
r_nbd_refined0.218
r_symmetry_hbond_refined0.174
r_xyhbond_nbd_refined0.165
r_chiral_restr0.121
r_bond_refined_d0.02
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2009
Nucleic Acid Atoms
Solvent Atoms228
Heterogen Atoms7

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling