3BCN
Crystal structure of a papain-like cysteine protease Ervatamin-A complexed with irreversible inhibitor E-64
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.5 | 293 | 0.2M Lithium acetate dihydrate, 20%(w/v) PEG 3350, 12% Glycerol, pH 7.5, VAPOR DIFFUSION, temperature 293K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.6 | 52.76 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 31.168 | α = 90 |
b = 105.587 | β = 101.96 |
c = 73.927 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 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 | IMAGE PLATE | MAR scanner 345 mm plate | Mar multilayer confocal system | 2007-10-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.5 | 100 | 85.8 | 0.0743 | 5.4 | 1.97 | 14392 | 13929 | 42.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.5 | 2.56 | 81.4 | 0.1463 | 3 | 2.04 | 914 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2PNS | 2.85 | 30 | 10943 | 8207 | 460 | 75 | 0.2398 | 0.2398 | 0.27 | CNS SCRIPT MAKE_CV_TWIN.INP, ENSURES THAT TWIN-RELATED PAIRS OF REFLECTIONS ARE EITHER BOTH IN TEST OR BOTH IN WORK SET |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 25.5 |
c_angle_deg | 1.5 |
c_improper_angle_d | 1.16 |
c_bond_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3208 |
Nucleic Acid Atoms | |
Solvent Atoms | 40 |
Heterogen Atoms | 54 |
Software
Software | |
---|---|
Software Name | Purpose |
CNS | refinement |
MAR345dtb | data collection |
AUTOMAR | data reduction |
AMoRE | phasing |