2XJM
Crystal structure of Streptococcus suis Dpr with cobalt
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 7.4 | 30 - 35 % (V/V) PEG 400, 0.2 M CACL2, 0.1 M HEPES-NAOH (PH 7.4) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 104.96 | α = 90 |
b = 137.42 | β = 90 |
c = 141.95 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | MARRESEARCH MARMOSAIC | VERTICALLY FOCUSSING | 2008-10-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X12 | EMBL/DESY, HAMBURG | X12 |
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 | 2.3 | 25 | 96.2 | 0.05 | 16.6 | 3.1 | 88486 | 2 | 43.3 |
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) | |||||||||||
1 | 2.3 | 2.36 | 76.9 | 0.11 | 7.4 | 2.3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | OTHER | THROUGHOUT | NONE | 2.3 | 24.91 | 84061 | 4425 | 100 | 0.17986 | 0.17671 | 0.2403 | RANDOM | 19.295 |
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] | |
-0.31 | -0.19 | 0.51 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 44.628 |
r_dihedral_angle_4_deg | 17.06 |
r_dihedral_angle_3_deg | 15.857 |
r_dihedral_angle_1_deg | 5.005 |
r_scangle_it | 3.441 |
r_scbond_it | 2.155 |
r_angle_refined_deg | 1.289 |
r_mcangle_it | 1.133 |
r_mcbond_it | 0.57 |
r_chiral_restr | 0.085 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14438 |
Nucleic Acid Atoms | |
Solvent Atoms | 802 |
Heterogen Atoms | 83 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |