3IIZ
X-ray structure of the FeFe-hydrogenase maturase HydE from T. maritima in complex with S-adenosyl-L-methionine
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 294 | PEG 4000, LISO4, TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.15 | 42.75 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 50.628 | α = 90 |
| b = 78.78 | β = 90 |
| c = 85.943 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
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 4 | 2005-06-20 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.934 | ESRF | ID14-1 |
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 | 1.62 | 43 | 93.5 | 0.066 | 13.39 | 2.5 | 41143 | 14 | |||||||||||
| 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) | |||||||||||
| 1.62 | 1.72 | 72.9 | 0.369 | 2.38 | 1.45 | 13887 | |||||||||||||
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 3CIW | 1.62 | 38.16 | 41143 | 2204 | 97.58 | 0.1399 | 0.13754 | 0.18438 | RANDOM | 12.188 | ||||||
| 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] | |
| 0.62 | 0.06 | -0.67 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.806 |
| r_dihedral_angle_4_deg | 15.901 |
| r_dihedral_angle_3_deg | 12.335 |
| r_dihedral_angle_1_deg | 11.92 |
| r_sphericity_free | 5.306 |
| r_scangle_it | 3.374 |
| r_scbond_it | 2.496 |
| r_sphericity_bonded | 2.43 |
| r_angle_refined_deg | 1.749 |
| r_mcangle_it | 1.616 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2822 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 446 |
| Heterogen Atoms | 198 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| ProDC | data collection |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| REFMAC | phasing |
