1N1G
Crystal structure of Leishmania mexicana Glycerol-3-phosphate dehydrogenase with inhibitor BCP
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | NaCitrate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.32 | 63 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 70.421 | α = 90 |
| b = 70.421 | β = 90 |
| c = 210.908 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 150 | CCD | ADSC QUANTUM 4 | 2002-07-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 1.0 | ALS | 5.0.2 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.5 | 67 | 99.5 | 0.11 | 0.11 | 5 | 14.9 | 18236 | 18150 | 43.6 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 2.5 | 2.64 | 94.5 | 0.427 | 0.427 | 1.6 | 2.5 | 2866 | |||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.5 | 18.52 | 18236 | 18150 | 983 | 99.53 | 0.2072 | 0.20728 | 0.20599 | 0.23144 | RANDOM | 41.571 | |||||
| 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] | |
| 1.05 | 1.05 | -2.1 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_1_deg | 4.825 |
| r_scangle_it | 2.902 |
| r_scbond_it | 1.641 |
| r_angle_refined_deg | 1.557 |
| r_mcangle_it | 1.146 |
| r_mcbond_it | 0.585 |
| r_symmetry_hbond_refined | 0.419 |
| r_nbd_refined | 0.186 |
| r_symmetry_vdw_refined | 0.184 |
| r_xyhbond_nbd_refined | 0.104 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2599 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 81 |
| Heterogen Atoms | 51 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-2000 | data collection |
| SCALA | data scaling |
| AMoRE | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| CCP4 | data scaling |
