Crystal Structure of Calcium-bound D,D-heptose 1.7-bisphosphate phosphatase from E. Coli
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2GMW | PDB Entry 2gmw |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.8 | 298 | 25% PEG 3350, 0.1M Tris, 0.005M DTT, 0.025M sodium chloride, 0.005M calcium chloride, 11% glycerol , pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.81 | 32.08 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 63.904 | α = 90 |
| b = 50.585 | β = 90 |
| c = 52.638 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 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 | IMAGE PLATE | RIGAKU RAXIS IV++ | mirrors | 2008-09-08 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU RU300 | 1.54 | ||
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 | 1.7 | 40.62 | 94.2 | 0.047 | 13.9 | 3.64 | 18244 | 1 | 1 | 26.075 | |||||||||
| 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 | 1.7 | 1.76 | 80 | 0.313 | 3.2 | 2.36 | 1894 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | 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 Selection Details | Mean Isotropic B | ||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB Entry 2gmw | 1.7 | 40.62 | 1 | 1 | 17299 | 17299 | 944 | 94.15 | 0.2032 | 0.20045 | 0.2 | 0.25844 | RANDOM | 29.588 | ||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
| -1.22 | -0.58 | 1.8 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.501 |
| r_dihedral_angle_4_deg | 20.815 |
| r_dihedral_angle_3_deg | 12.846 |
| r_dihedral_angle_1_deg | 6.729 |
| r_scangle_it | 3.622 |
| r_scbond_it | 2.502 |
| r_angle_refined_deg | 1.504 |
| r_mcangle_it | 1.376 |
| r_mcbond_it | 0.885 |
| r_nbtor_refined | 0.301 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1423 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 192 |
| Heterogen Atoms | 2 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CrystalClear | data collection |
| PHENIX | model building |
| REFMAC | refinement |
| CrystalClear | data reduction |
| CrystalClear | data scaling |
| PHENIX | phasing |
