7JVZ | pdb_00007jvz

SARS CoV-2 MAIN PROTEASE 3CLpro, ROOM TEMPERATURE, DAMAGE FREE XFEL MONOCLINIC STRUCTURE


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Y2E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.529312.5 % PEG 3350, 100 mmol/L bistris
Crystal Properties
Matthews coefficientSolvent content
2.1643.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.6α = 90
b = 55.4β = 100.5
c = 45.6γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELSLAC ePix10k2020-08-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.26SLAC LCLSMFX

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1MESHinjection
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
140 (fs)12019.8 (KeV)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.2331000.945519428
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.30.181.77

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT6y2e2.532.67896146793.160.174510.172270.190.217190.22RANDOM64.784
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]
-1.560.96-0.71.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.079
r_dihedral_angle_3_deg20.553
r_dihedral_angle_4_deg17.852
r_long_range_B_refined14.02
r_long_range_B_other13.935
r_mcangle_it9.544
r_mcangle_other9.541
r_scangle_other9.529
r_dihedral_angle_1_deg8.47
r_mcbond_it6.444
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.079
r_dihedral_angle_3_deg20.553
r_dihedral_angle_4_deg17.852
r_long_range_B_refined14.02
r_long_range_B_other13.935
r_mcangle_it9.544
r_mcangle_other9.541
r_scangle_other9.529
r_dihedral_angle_1_deg8.47
r_mcbond_it6.444
r_mcbond_other6.444
r_scbond_other6.207
r_scbond_it6.206
r_angle_refined_deg1.752
r_angle_other_deg1.235
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms2367
Nucleic Acid Atoms
Solvent Atoms46
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling