4KAG
Crystal structure analysis of a single amino acid deletion mutation in EGFP
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 6.5 | 291 | 0.1 M Na cacodylate, 0.2 M NaCl, 1M Na citrate, pH 6.5, VAPOR DIFFUSION, temperature 291K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.38 | 48.23 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 57.14 | α = 90 |
| b = 57.14 | β = 90 |
| c = 135.33 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 32 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 | M | SINGLE WAVELENGTH | ||||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97630 | Diamond | I03 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.12 | 39.94 | 97.3 | 9.1 | 91397 | ||||||||||||||
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 4EUL | 1.12 | 39.94 | 89439 | 4723 | 96.12 | 0.14509 | 0.14426 | 0.16108 | RANDOM | 15.08 | ||||||
| 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] | |
| 0.13 | 0.13 | 0.13 | -0.43 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.795 |
| r_dihedral_angle_4_deg | 19.681 |
| r_dihedral_angle_3_deg | 13.13 |
| r_rigid_bond_restr | 10.307 |
| r_dihedral_angle_1_deg | 7.925 |
| r_angle_other_deg | 3.936 |
| r_angle_refined_deg | 2.715 |
| r_sphericity_bonded | 1.217 |
| r_chiral_restr | 0.148 |
| r_bond_refined_d | 0.03 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1802 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 280 |
| Heterogen Atoms | 98 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SCALA | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
