1VL8
Crystal structure of Gluconate 5-dehydrogenase (TM0441) from Thermotoga maritima at 2.07 A resolution
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1G6K | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 4.2 | 277 | Acetate pH 4.2, 35% Glycerol, 0.4M NH4H2PO3 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.89 | 68.14 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 123.504 | ¦Á = 90 |
| b = 123.504 | ¦Â = 90 |
| c = 122.323 | ¦Ã = 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 | CCD | APS | water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror | 2004-02-20 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 19-BM | APS | 19-BM | |
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 | 1.96 | 50 | 89.42 | 0.088 | 16.01 | 6.89 | 61222 | 32.51 | |||||||||||
| 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 | 1.96 | 2.03 | 72.83 | 0.672 | 1.06 | 2.35 | 4917 | ||||||||||||
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 | 1g6k | 2.07 | 43.67 | 50440 | 2715 | 91.5 | 0.15148 | 0.14999 | 0.17955 | RANDOM | 26.843 | ||||||
| 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] | |
| -1.08 | -1.08 | 2.16 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.122 |
| r_dihedral_angle_4_deg | 14.893 |
| r_dihedral_angle_3_deg | 13.495 |
| r_scangle_it | 6.908 |
| r_dihedral_angle_1_deg | 5.97 |
| r_scbond_it | 5.163 |
| r_mcangle_it | 2.492 |
| r_mcbond_it | 2.181 |
| r_angle_refined_deg | 1.655 |
| r_angle_other_deg | 0.947 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3838 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 331 |
| Heterogen Atoms | 102 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
