5RLZ

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2293643386


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
2.3447.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.208α = 102.74
b = 70.39β = 95.87
c = 85.354γ = 112.42
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-07-29SINGLE 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
11.9781.4596.40.0860.1030.0550.9986.43.482548
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)
11.972.01892.122.5631.4130.2633.14367

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 SYNTHESISTHROUGHOUT6ZSL1.9781.4673857400190.970.22420.22150.2734RANDOM53.257
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]
0.87-0.61-1.79-2.44-0.783.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.971
r_dihedral_angle_4_deg18.257
r_dihedral_angle_3_deg14.962
r_dihedral_angle_1_deg7.289
r_mcangle_it6.64
r_mcbond_other4.258
r_mcbond_it4.257
r_angle_refined_deg1.473
r_angle_other_deg1.213
r_chiral_restr0.058
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.971
r_dihedral_angle_4_deg18.257
r_dihedral_angle_3_deg14.962
r_dihedral_angle_1_deg7.289
r_mcangle_it6.64
r_mcbond_other4.258
r_mcbond_it4.257
r_angle_refined_deg1.473
r_angle_other_deg1.213
r_chiral_restr0.058
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8917
Nucleic Acid Atoms
Solvent Atoms454
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing