3P06
Crystal structure of Tellina virus 1 VP4 protease in the form of an intra-molecular(cis)acyl-enzyme complex.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 5 | 296 | reservoir: 21% PEG8000, 0.55M ammonium sulfate. drop: On a coverslip, 1 microliter of VP4 was mixed with 1 microliter of reservoir reagent(21% PEG8000, 0.55M ammonium sulfate) and 1 microliter of 0.2M urea as additive. To aid in crystal nucleation, this drop was seeded with 1 microliter of selenomethionine- labelled crystal from an older drop, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.55 | 51.86 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 59.14 | α = 90 |
b = 59.14 | β = 90 |
c = 208.142 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 64 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | DCM WITH CRYO-COOLED 1ST CRYSTAL SAGITTALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR. | 2010-05-28 | M | SAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | CLSI | 08ID-1 |
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 | 2.1 | 52 | 99.8 | 0.107 | 14.5 | 11.4 | 13466 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.1 | 2.2 | 98.5 | 0.35 | 0.3 | 4.3 | 5.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 2.1 | 52 | 13466 | 12743 | 662 | 99.7 | 0.185 | 0.182 | 0.233 | RANDOM | 28.44 |
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] | |
-0.02 | -0.01 | -0.02 | 0.03 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.944 |
r_dihedral_angle_4_deg | 17.371 |
r_dihedral_angle_3_deg | 15.683 |
r_scangle_it | 6.446 |
r_dihedral_angle_1_deg | 6.422 |
r_scbond_it | 3.965 |
r_mcangle_it | 2.126 |
r_angle_refined_deg | 1.979 |
r_mcbond_it | 1.186 |
r_chiral_restr | 0.138 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1424 |
Nucleic Acid Atoms | |
Solvent Atoms | 47 |
Heterogen Atoms | 32 |
Software
Software | |
---|---|
Software Name | Purpose |
Mx | data collection |
PHENIX | model building |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHENIX | phasing |