2R9U
Crystal Structure of Lamprey Variable Lymphocyte Receptor 2913 Ectodomain
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 295 | 2.0-2.4 M NaH2PO4/K2HPO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.64 | 53.47 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 72.109 | α = 90 |
| b = 61.057 | β = 107.35 |
| c = 98.081 | γ = 90 |
| Symmetry | |
|---|---|
| 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 | 100 | CCD | MarUSA MarMosaic -325 | Flat Mirror | 2007-06-03 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.98 | SSRL | BL9-2 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.1 | 50 | 91.3 | 0.115 | 9 | 3.1 | 43844 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.1 | 2.18 | 81.3 | 0.293 | 3 | 2.8 | 3847 | ||||||||||||
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2O6R | 2.1 | 50 | 41594 | 2232 | 91.06 | 0.22 | 0.217 | 0.264 | RANDOM | 20.107 | ||||||
| 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] | |
| 3.91 | -0.36 | -1.39 | -2.73 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.543 |
| r_dihedral_angle_4_deg | 23.63 |
| r_dihedral_angle_3_deg | 13.423 |
| r_dihedral_angle_1_deg | 6.324 |
| r_scangle_it | 5.945 |
| r_scbond_it | 4.526 |
| r_mcangle_it | 2.272 |
| r_angle_refined_deg | 1.654 |
| r_mcbond_it | 1.54 |
| r_angle_other_deg | 1.068 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5456 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 321 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| Blu-Ice | data collection |
| MOSFLM | data reduction |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| CaspR | phasing |
