6NAU
1.55 Angstrom Resolution Crystal Structure of 6-phosphogluconolactonase from Klebsiella pneumoniae
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 292 | Protein: 9.8 mg/ml, 0.01M Tris-HCl pH 8.3, Screen: PACT (F6), 0.2M Sodium formate, 0.1M Bis-Tris propane pH 6.5, 20% (w/v) PEG 3350 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.13 | 42.3 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 184.745 | α = 90 |
| b = 184.745 | β = 90 |
| c = 48.761 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 62 |
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 | MARMOSAIC 300 mm CCD | C(111) | 2018-06-06 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.9787 | APS | 21-ID-F |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.55 | 30 | 100 | 0.1 | 0.1 | 0.106 | 0.035 | 20.5 | 9.8 | 138516 | -3 | 12.8 | |||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
| 1 | 1.55 | 1.58 | 100 | 0.711 | 0.711 | 0.757 | 0.258 | 0.861 | 3.2 | 8.5 | |||||||||
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 | 4QRJ | 1.55 | 29.33 | 131376 | 6945 | 99.98 | 0.12721 | 0.12569 | 0.15552 | RANDOM | 12.521 | ||||||
| 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] | |
| 0.07 | 0.04 | 0.07 | -0.24 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 30.869 |
| r_dihedral_angle_4_deg | 17.193 |
| r_dihedral_angle_3_deg | 10.217 |
| r_dihedral_angle_1_deg | 5.515 |
| r_long_range_B_refined | 4.998 |
| r_long_range_B_other | 4.513 |
| r_scangle_other | 3.337 |
| r_scbond_it | 2.187 |
| r_scbond_other | 2.187 |
| r_mcangle_it | 1.426 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 7698 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1779 |
| Heterogen Atoms | 83 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| MoRDa | phasing |
