Xylulose 5-phosphate phosphoketolase from Lactococcus lactis
X-RAY DIFFRACTION - SOLUTION SCATTERING
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1TRK | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, HANGING DROP | | 291 | 17 % (w/v) PEG-3350, 0.2 M sodium isothiocyanate, |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.34 | 47.4 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 158.1 | α = 90 |
| b = 141.5 | β = 90.29 |
| c = 161.15 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 1 21 1 |
|---|
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 | MAR CCD 130 mm | | 2005-05-21 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | ESRF BEAMLINE ID13 | 0.931 | ESRF | ID13 |
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) | CC (Half) | R Split (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 | 1.95 | 44.3 | 97.3 | | | 0.152 | 0.079 | 0.995 | | 6.79 | 3.5 | | 501022 | | | 23.3 |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.95 | 2 | | | | 0.913 | 0.548 | 0.183 | | 1.27 | 2.5 | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | 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 (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.95 | 44.3 | | | | 500681 | 25031 | 97.3 | | | 0.212 | 0.21 | 0.261 | 0.26 | Random selection | 28.9 |
| 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] |
|---|
| | | | | |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 52634 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 5998 |
| Heterogen Atoms | 256 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| MOLREP | phasing |
