3PW3
Crystal structure of a cysteine protease (BDI_2249) from Parabacteroides distasonis ATCC 8503 at 2.23 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.2 | 293 | 20.00% polyethylene glycol 3350, 0.2000M potassium sodium tartrate, No Buffer pH 7.2, Additive: 0.001 M zinc chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.03 | 59.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 104.592 | α = 90 |
b = 137.81 | β = 90 |
c = 223.165 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 325 mm CCD | flat collimating Rh coated mirror, toroidal focussing mirror | 2010-07-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL14-1 | SSRL | BL14-1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.23 | 29.966 | 98.7 | 0.073 | 13.23 | 154800 | -3 | 38.695 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1 | 2.23 | 2.31 | 99.6 | 0.534 | 2.6 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.23 | 29.966 | 154749 | 7771 | 98.36 | 0.1603 | 0.1592 | 0.1812 | RANDOM | 40.4993 |
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] | |
-0.61 | 0.23 | 0.39 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.573 |
r_dihedral_angle_4_deg | 16.558 |
r_dihedral_angle_3_deg | 14.189 |
r_dihedral_angle_1_deg | 5.885 |
r_angle_refined_deg | 1.237 |
r_angle_other_deg | 1.109 |
r_chiral_restr | 0.078 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 17102 |
Nucleic Acid Atoms | |
Solvent Atoms | 2003 |
Heterogen Atoms | 87 |
Software
Software | |
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Software Name | Purpose |
SHELX | phasing |
REFMAC | refinement |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SHELXD | phasing |
autoSHARP | phasing |