5S27

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z1262398530


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP0.1293.1530% PEG 3K
Crystal Properties
Matthews coefficientSolvent content
2.141.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.377α = 90
b = 88.377β = 90
c = 39.082γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-07-22SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91258DiamondI04-1

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
11.0588.498.50.1160.1280.0520.9973.65.113891012.89
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)
11.051.0782.22.4853.1441.8830.2462.25658

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 SYNTHESISTHROUGHOUTNone1.12688.3892560471380.90.18120.17930.2166RANDOM20.78
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]
3.22833.2283-6.4566
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion15.78
t_omega_torsion3.96
t_angle_deg1.08
t_bond_d0.01
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_trig_c_planes
t_utility_distance
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion15.78
t_omega_torsion3.96
t_angle_deg1.08
t_bond_d0.01
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_trig_c_planes
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
t_dihedral_angle_d
t_gen_planes
t_it
t_sum_occupancies
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2527
Nucleic Acid Atoms
Solvent Atoms367
Heterogen Atoms15

Software

Software
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing