5IEL
Structure of Lysozyme labeled with fluorescein isothiocyanate (FITC) at 1.15 Angstroms resolution
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4NGI | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 285 | 0.1M HEPES 30% v/v Jeffamine ED-2001 ; 0.2M Magnesium nitrate hexahydrate 20% w/v Polyethylene glycol 3,350 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.08 | 40.86 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 80.756 | α = 90 |
| b = 80.756 | β = 90 |
| c = 36.561 | 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 | 100 | PIXEL | DECTRIS PILATUS3 6M | 2015-09-17 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.97241 | ESRF | ID14-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.15 | 57.1 | 99.9 | 0.05 | 0.05 | 16.5 | 6.5 | 43530 | 2 | 12.6 | |||||||||
| 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 | 1.15 | 1.18 | 99.9 | 0.4 | 1.76 | 6.9 | |||||||||||||
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 | 4NGI | 1.15 | 57.1 | 41269 | 2184 | 99.93 | 0.149 | 0.14754 | 0.17577 | RANDOM | 17.973 | ||||||
| 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] | |
| -0.12 | -0.12 | 0.24 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.22 |
| r_sphericity_free | 36.073 |
| r_dihedral_angle_4_deg | 14.52 |
| r_sphericity_bonded | 13.889 |
| r_dihedral_angle_3_deg | 12.243 |
| r_rigid_bond_restr | 8.231 |
| r_dihedral_angle_1_deg | 6.388 |
| r_scbond_it | 4.46 |
| r_long_range_B_refined | 3.656 |
| r_angle_refined_deg | 2.265 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1001 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 174 |
| Heterogen Atoms | 28 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| iMOSFLM | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
