5RML

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z85956652


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529316 % Ethylene Glycol, 8 % PEG 8K, 0.05 M HEPES, 0.05 M MOPS, 0.03 M Sodium Nitrate, 0,03 M Sodium Phosphate, 0.03 M Ammonium Sulphate
Crystal Properties
Matthews coefficientSolvent content
2.3347.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.94α = 102.81
b = 70.101β = 95.84
c = 85.447γ = 112.42
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-07-30SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9126DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.4281.4797.20.1210.1440.0770.9696.33.444396
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.422.5295.41.3831.6530.890.3353.44584

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT6ZSL2.4381.52420062298970.21120.2070.2885RANDOM59.33
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]
0.88-0.48-2.47-1.37-12.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.091
r_dihedral_angle_4_deg17.44
r_dihedral_angle_3_deg15.691
r_mcangle_it8.828
r_dihedral_angle_1_deg7.777
r_mcbond_it5.81
r_mcbond_other5.808
r_angle_refined_deg1.611
r_angle_other_deg1.235
r_chiral_restr0.063
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.091
r_dihedral_angle_4_deg17.44
r_dihedral_angle_3_deg15.691
r_mcangle_it8.828
r_dihedral_angle_1_deg7.777
r_mcbond_it5.81
r_mcbond_other5.808
r_angle_refined_deg1.611
r_angle_other_deg1.235
r_chiral_restr0.063
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8917
Nucleic Acid Atoms
Solvent Atoms453
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing