7I16 | pdb_00007i16

PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment C07 from the F2X-Entry Screen in orthorhombic space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7BB2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.72910.2 M MIB (sodium malonate, imidazole, and boric acid in the molar ratios 2:3:3) pH 7.7, 23.5 % PEG 1500, 5 % DMSO, 1 mM DTT. Crystal seeds were used to ensure reproducible crystal growth.
Crystal Properties
Matthews coefficientSolvent content
2.5651.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.67α = 90
b = 98.94β = 90
c = 103.18γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2022-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

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
12.1349.1298.40.2010.2210.9926.6938752
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)
12.132.2698.91.4641.6010.474

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.1349.1236814193898.390.229350.22710.23130.273080.2749RANDOM36.982
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]
-1.03-0.131.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.545
r_dihedral_angle_4_deg18.544
r_dihedral_angle_3_deg14.878
r_dihedral_angle_1_deg7.816
r_long_range_B_other7.554
r_long_range_B_refined7.549
r_scangle_other5.032
r_mcangle_it4.503
r_mcangle_other4.503
r_scbond_it3.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.545
r_dihedral_angle_4_deg18.544
r_dihedral_angle_3_deg14.878
r_dihedral_angle_1_deg7.816
r_long_range_B_other7.554
r_long_range_B_refined7.549
r_scangle_other5.032
r_mcangle_it4.503
r_mcangle_other4.503
r_scbond_it3.12
r_scbond_other3.119
r_mcbond_it2.885
r_mcbond_other2.883
r_angle_refined_deg1.497
r_angle_other_deg1.302
r_chiral_restr0.063
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms4697
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing