4OM4
Crystal structure of CTX A2 from Taiwan Cobra (Naja naja atra)
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2BHI | PDB ENTRY 2BHI |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | 291 | 5.5 M ammonium nitrate, 0.1 M Bis-Tris, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.28 | 71.25 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 107.412 | α = 90 |
| b = 107.412 | β = 90 |
| c = 100.256 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 200 | CCD | ADSC QUANTUM 315 | 2009-08-04 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | NSRRC BEAMLINE BL13B1 | 1 | NSRRC | BL13B1 |
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 | 2.74 | 30 | 99.9 | 0.103 | 13.2 | 15.5 | 15886 | 15865 | 2 | 2 | |||||||||
| 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 | 2.74 | 2.84 | 100 | 0.494 | 15 | ||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2BHI | 2.74 | 25.62 | 15886 | 15030 | 792 | 99.58 | 0.19979 | 0.1966 | 0.2 | 0.2596 | 0.25 | RANDOM | 44.846 | |||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
| -2.31 | -2.31 | 4.62 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.63 |
| r_dihedral_angle_4_deg | 24.847 |
| r_dihedral_angle_3_deg | 23.129 |
| r_dihedral_angle_1_deg | 7.743 |
| r_mcangle_it | 5.152 |
| r_scbond_it | 3.746 |
| r_mcbond_it | 3.368 |
| r_mcbond_other | 3.36 |
| r_angle_refined_deg | 1.914 |
| r_angle_other_deg | 0.877 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2325 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 92 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
