7HUC
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment B07 from the F2X-Entry Screen in monoclinic space group
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6Y2E |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.7 | 291 | 0.2 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 coefficient | Solvent content |
1.9 | 35 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 113.4 | ¦Á = 90 |
b = 53.09 | ¦Â = 102.58 |
c = 44.41 | ¦Ã = 90 |
Symmetry | |
---|---|
Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 2M | 2022-04-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 0.9184 | BESSY | 14.2 |
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) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||
1 | 1.52 | 47.91 | 99.2 | 0.081 | 0.08900000000000001 | 0.9990000000000001 | 12.91 | 39439 |
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) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.52 | 1.61 | 98.4 | 1.7730000000000001 | 1.944 | 0.486 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (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 Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.52 | 47.91 | 37466 | 1972 | 99.26 | 0.2045 | 0.20293 | 0.2117 | 0.23494 | 0.243 | RANDOM | 25.958 |
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] | |
1.52 | -0.43 | 0.25 | -1.44 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 13.617 |
r_dihedral_angle_1_deg | 7.241 |
r_dihedral_angle_2_deg | 5.835 |
r_long_range_B_other | 5.779 |
r_long_range_B_refined | 5.774 |
r_scangle_other | 4.528 |
r_scbond_it | 3.264 |
r_scbond_other | 3.263 |
r_mcangle_it | 2.975 |
r_mcangle_other | 2.975 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2368 |
Nucleic Acid Atoms | |
Solvent Atoms | 93 |
Heterogen Atoms | 38 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data scaling |
XDS | data reduction |
PHASER | phasing |