4KDV
Crystal structure of a bacterial immunoglobulin-like domain from the M. primoryensis ice-binding adhesin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 4.5 | 298 | 0.2M calcium acetate, 0.1 M sodium acetate and 30% (v/v) PEG, microbatch, temperature 298.0K , pH 4.5, EVAPORATION |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.59 | 22.95 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 28.69 | α = 90 |
b = 43.02 | β = 96.91 |
c = 32.26 | γ = 90 |
Symmetry | |
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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 | 93 | IMAGE PLATE | RIGAKU RAXIS IV++ | MULTILAYER CONFOCAL | 2012-10-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF |
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 | 2.42 | 25.7 | 91 | 0.079 | 15.36 | 3.8 | 5343 | 21.3 |
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 | 2.42 | 2.57 | 80.4 | 0.095 | 11.15 |
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 | 2.42 | 25.7 | 2999 | 2605 | 120 | 89.5 | 0.149 | 0.144 | 0.234 | RANDOM | 20.67 |
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] | |
-0.6 | 1.3 | 1.72 | -1.24 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.396 |
r_dihedral_angle_3_deg | 13.699 |
r_dihedral_angle_1_deg | 6.308 |
r_angle_refined_deg | 1.54 |
r_angle_other_deg | 0.757 |
r_chiral_restr | 0.069 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.004 |
r_bond_other_d | 0.001 |
r_gen_planes_other | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 691 |
Nucleic Acid Atoms | |
Solvent Atoms | 66 |
Heterogen Atoms | 5 |
Software
Software | |
---|---|
Software Name | Purpose |
StructureStudio | data collection |
PHENIX | model building |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHENIX | phasing |