4PSY
100K crystal structure of Escherichia coli dihydrofolate reductase
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1RX2 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 17% PEG 400, 20 mM imidazole pH 7.0, 125 mM MnCl2, VAPOR DIFFUSION, HANGING DROP | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.07 | 40.62 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 33.96 | α = 90 |
| b = 44.823 | β = 90 |
| c = 98.254 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
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 | 2005-04-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.9 | SSRL | BL11-1 |
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 | 0.85 | 40.8 | 98.2 | 0.049 | 36.3 | 5.5 | 130200 | 130200 | -3 | -3 | 7.68 | ||||||||
| 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 | 0.85 | 0.88 | 97.2 | 0.55 | 2.3 | 4 | 12715 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | FREE R | 1RX2 | 0.85 | 40.8 | 130053 | 130053 | 6501 | 98.3 | 0.1128 | 0.1125 | 0.1125 | 0.128 | RANDOM | |||||
| 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 |
| 89 | 1193 | 1673.94 |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| s_from_restr_planes | 0.376 |
| s_angle_d | 0.315 |
| s_approx_iso_adps | 0.1394 |
| s_non_zero_chiral_vol | 0.0996 |
| s_zero_chiral_vol | 0.0902 |
| s_similar_adp_cmpnt | 0.0431 |
| s_anti_bump_dis_restr | 0.0311 |
| s_bond_d | 0.0116 |
| s_similar_dist | |
| s_rigid_bond_adp_cmpnt | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1270 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 356 |
| Heterogen Atoms | 82 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| ADSC | data collection |
| SHELX | model building |
| SHELXL-97 | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| SHELX | phasing |
