2ZXE
Crystal structure of the sodium - potassium pump in the E2.2K+.Pi state
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3B8E | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | Dialysis | 7 | 298 | pH 7.0, Dialysis, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.08 | 60.04 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 223.815 | α = 90 |
| b = 50.914 | β = 105.12 |
| c = 163.786 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 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 | ADSC QUANTUM 315 | M | SINGLE WAVELENGTH | |||||||
| 2 | 1 | CCD | RAYONIX MX225HE | |||||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 0.9 | SPring-8 | BL41XU |
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 | 2.4 | 50 | 99.1 | 0.058 | 38.8 | 17 | 70710 | 70074 | |||||||||||
| 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 | 2.4 | 2.46 | 95.7 | 0.372 | 2.8 | 5.8 | 5155 | ||||||||||||
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 | THROUGHOUT | 3B8E | 2.4 | 15 | 66157 | 3555 | 100 | 0.24772 | 0.24644 | 0.27124 | RANDOM | 59.782 | |||||||
| 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] | |
| 2.05 | -1.99 | 0.01 | -3.1 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 38.775 |
| r_dihedral_angle_4_deg | 15.787 |
| r_dihedral_angle_3_deg | 14.955 |
| r_dihedral_angle_1_deg | 4.084 |
| r_scangle_it | 1.467 |
| r_angle_refined_deg | 1.085 |
| r_mcangle_it | 1.032 |
| r_scbond_it | 0.863 |
| r_mcbond_it | 0.564 |
| r_chiral_restr | 0.068 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 10131 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 130 |
| Heterogen Atoms | 79 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| CNS | phasing |
