4KDW
Crystal structure of a bacterial immunoglobulin-like domain from the M. primoryensis ice-binding adhesin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 8.5 | 298 | 20% PEG 4000, 0.2M CaCl2, 0.1M Tris-HCl, microbatch, pH 8.5, EVAPORATION, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.72 | 28.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 25.64 | α = 97.02 |
b = 28.62 | β = 112.93 |
c = 32.25 | γ = 96.88 |
Symmetry | |
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Space Group | P 1 |
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 | 93 | CCD | MARMOSAIC 300 mm CCD | 2012-12-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | APS | 23-ID-B |
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 | 1.35 | 29.191 | 95.1 | 0.049 | 10.33 | 3.6 | 17224 | 7.4 |
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 | 1.35 | 1.42 | 91.6 | 0.085 | 10.7 | 3.2 |
Refinement
Statistics | |||||||||||||||||||
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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 | PDB ENTRY 4KDV | 1.35 | 29.19 | 16337 | 16337 | 887 | 95.1 | 0.132 | 0.13 | 0.165 | RANDOM | 9.71 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.54 | 0.21 | 0.06 | 0.03 | 0.21 | -0.46 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.989 |
r_dihedral_angle_3_deg | 8.704 |
r_dihedral_angle_1_deg | 6.228 |
r_angle_refined_deg | 2.244 |
r_angle_other_deg | 0.927 |
r_chiral_restr | 0.128 |
r_bond_refined_d | 0.025 |
r_gen_planes_refined | 0.01 |
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 | 140 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
JBluIce-EPICS | data collection |
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |