3M9Z
Crystal Structure of extracellular domain of mouse NKR-P1A
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.2 | 291 | 0.3M Ammonium phosphate, not buffered, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.912 | α = 90 |
b = 59.912 | β = 90 |
c = 159.303 | γ = 90 |
Symmetry | |
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Space Group | I 41 2 2 |
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 225 mm CCD | MIRRORS, Microdiffractometer MD2 | 2009-05-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.918 | BESSY | 14.1 |
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 | 1.7 | 15 | 99.7 | 0.07 | 14.3 | 7.4 | 16416 | -999 | -999 | 24.1 |
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 | 1.7 | 1.79 | 99 | 0.704 | 2.1 | 5.3 | 2319 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1E87 | 1.7 | 15 | 16396 | 16396 | 829 | 99.81 | 0.19696 | 0.19696 | 0.19481 | 0.23927 | RANDOM | 23.297 |
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] | |
0.36 | 0.36 | -0.73 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.242 |
r_dihedral_angle_3_deg | 15.747 |
r_dihedral_angle_4_deg | 10.775 |
r_dihedral_angle_1_deg | 5.928 |
r_scangle_it | 3.833 |
r_scbond_it | 2.649 |
r_mcangle_it | 2.356 |
r_angle_refined_deg | 1.741 |
r_mcbond_it | 1.331 |
r_angle_other_deg | 0.92 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1005 |
Nucleic Acid Atoms | |
Solvent Atoms | 111 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
BALBES | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |