6EFH
Pyruvate decarboxylase from Kluyveromyces lactis soaked with pyruvamide
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.25 | 281.15 | 2 mg/mL KlPDC in 2 mM MES, 18 mM citrate, pH 6.25, 4 mM thiamine diphosphate, 4 mM magnesium sulfate, 2 mM DTT, 1:1 with mother liquor (18-24% w/v PEG2000/PEG6000), ~25 days at 8 degrees C, soaked for 50 seconds in 2 uL mother liquor + 2 uL 90% v/v PEG400, 200 mM pyruvamide prior to flash freezing |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.22 | 61.8 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 172.765 | α = 90 |
| b = 172.765 | β = 90 |
| c = 210.083 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 4 2 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 | ADSC QUANTUM 4 | 2007-07-07 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | 0.93300 | ESRF | ID14-2 |
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 | 2.99 | 55.6 | 100 | 0.333 | 9 | 14.4 | 32279 | 25.68 | |||||||||||
| 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 | 2.99 | 3.05 | 100 | 1.797 | 1.6 | 14.7 | |||||||||||||
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 2VK4 | 2.99 | 55.6 | 31223 | 1055 | 100 | 0.181 | 0.178 | 0.265 | RANDOM | 42.52 | ||||||
| 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] | |
| 1.94 | 1.94 | -3.89 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.609 |
| r_dihedral_angle_4_deg | 20.327 |
| r_dihedral_angle_3_deg | 19.268 |
| r_dihedral_angle_1_deg | 8.406 |
| r_long_range_B_refined | 7.526 |
| r_long_range_B_other | 7.526 |
| r_mcangle_it | 5.17 |
| r_mcangle_other | 5.169 |
| r_scangle_other | 4.882 |
| r_mcbond_it | 3.213 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 8587 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 41 |
| Heterogen Atoms | 84 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| xia2 | data reduction |
| MOSFLM | data reduction |
| Aimless | data scaling |
| MOLREP | phasing |
