Initial structural analysis of Plasmodium falciparum Glycerol-3-phosphate dehydrogenase
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 10 | 293 | PEG 400, Potassium phosphate monobasic, CAPS, DTT, pH 10, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.3 | 71 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 177.455 | α = 90 |
| b = 177.455 | β = 90 |
| c = 232.699 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 63 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 210 | 2004-06-11 | M | SINGLE WAVELENGTH | ||||||
| 2 | 1 | x-ray | CCD | ADSC QUANTUM 210 | 2004-06-20 | M | MAD | |||||||
| 1,2 | 1 | |||||||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL11-3 | SSRL | BL11-3 | |
| 2 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 0.9794, 0.91840, 0.97950 | ALS | 8.2.1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.85 | 50 | 99.3 | 0.132 | 8.4 | 5.3 | 50738 | 50574 | -3 | 69.775 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1,2 | 2.85 | 3 | 96.3 | 0.708 | 1.8 | 4.3 | 7016 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | MAD | THROUGHOUT | 2.85 | 44.54 | 47958 | 47958 | 2557 | 99.05 | 0.23706 | 0.23706 | 0.23607 | 0.24 | 0.25576 | 0.26 | RANDOM | 56.225 | |||
| 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] | |
| -0.02 | -0.01 | -0.02 | 0.03 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.426 |
| r_dihedral_angle_3_deg | 14.926 |
| r_dihedral_angle_4_deg | 14.453 |
| r_dihedral_angle_1_deg | 4.761 |
| r_scangle_it | 2.229 |
| r_mcangle_it | 1.694 |
| r_scbond_it | 1.406 |
| r_mcbond_it | 1.011 |
| r_angle_refined_deg | 0.944 |
| r_angle_other_deg | 0.73 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 8415 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 10 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| CCP4 | data scaling |
| SHARP | phasing |
