3BH2
Structural Studies of Acetoacetate Decarboxylase
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5.95 | 281 | 40mM Phosphate buffer pH 5.95, 100mM Sarcosine, 15% PEG 3350, 18% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.73 | 54.99 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 104.07 | α = 90 |
| b = 104.07 | β = 90 |
| c = 578.094 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | H 3 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 315 | M | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | NSLS BEAMLINE X25 | 1.0000 | NSLS | X25 |
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 | 2.4 | 50 | 98.3 | 0.093 | 13 | 47172 | |||||||||||||
| 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) | |||||||||||
| 2.4 | 2.51 | 93.8 | 0.354 | 2.4 | |||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | 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 | THROUGHOUT | 2.4 | 45.79 | 41399 | 4638 | 97.6 | 0.20064 | 0.19581 | 0.19 | 0.24429 | 0.24 | RANDOM | 36.031 | |||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
| -0.03 | -0.02 | -0.03 | 0.05 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.03 |
| r_dihedral_angle_4_deg | 18.908 |
| r_dihedral_angle_3_deg | 18.641 |
| r_dihedral_angle_1_deg | 6.731 |
| r_scangle_it | 1.926 |
| r_angle_refined_deg | 1.283 |
| r_scbond_it | 1.14 |
| r_mcangle_it | 0.711 |
| r_mcbond_it | 0.41 |
| r_nbtor_refined | 0.307 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 7770 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 319 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PDB_EXTRACT | data extraction |
| CBASS | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| REFMAC | phasing |
| REFMAC | refinement |
