1TMM
Crystal structure of ternary complex of E.coli HPPK(W89A) with MGAMPCPP and 6-Hydroxymethylpterin
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1Q0N | PDB 1Q0N |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 4.6 | 292 | PEG4000, MAGNESIUM CHLORIDE, ACETATE, GLYCEROL, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K, pH 4.60 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.88 | 24.5 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 47.992 | α = 90 |
| b = 47.392 | β = 104.13 |
| c = 71.438 | 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 | ADSC QUANTUM 4 | MIRROR | 2000-10-02 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | NSLS BEAMLINE X9B | NSLS | X9B | |
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 | 1.25 | 30 | 99.8 | 0.078 | 16.8 | 4.037 | 85986 | 14.4 | |||||||||||
| 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 | 1.25 | 1.29 | 99.3 | 0.602 | 2 | 3.47 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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 | FREE R | PDB 1Q0N | 1.25 | 30 | 4 | 81812 | 4128 | 95 | 0.132 | 0.164 | RANDOM | 16.7 | ||||||
| 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] | |
| Coordinate Error | ||
|---|---|---|
| Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
| 14 | 2430 | 3294.5 |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| s_approx_iso_adps | 0.09 |
| s_anti_bump_dis_restr | 0.089 |
| s_non_zero_chiral_vol | 0.071 |
| s_zero_chiral_vol | 0.066 |
| s_similar_adp_cmpnt | 0.053 |
| s_from_restr_planes | 0.03 |
| s_angle_d | 0.029 |
| s_bond_d | 0.012 |
| s_rigid_bond_adp_cmpnt | 0.005 |
| s_similar_dist | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2516 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 652 |
| Heterogen Atoms | 126 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SHELX | model building |
| SHELXL-97 | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| AMoRE | phasing |
