Neutron crystal Structure of E.coli Dihydrofolate Reductase complexed with folate and NADP+
X-RAY DIFFRACTION - NEUTRON 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, SITTING DROP | 7 | 291 | 40mg/mL DHFR-folate-NADP+ complex, 12% (v/v) PEG400, 100 mM MnCl2, 20 mM imidazole, pH7.0 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.15 | 42.75 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 34.293 | α = 90 |
| b = 45.625 | β = 90 |
| c = 98.974 | 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 | 291 | IMAGE PLATE | RIGAKU | mirrors | 2013-09-10 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 291 | | CUSTOM-MADE | mirrors | 2013-08-10 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU | 1.54 | | |
| 2 | NUCLEAR REACTOR | OTHER | 3.3 | | |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 | 1.599 | 30 | 79.3 | | 0.188 | | | | | 5.3 | 7.5 | | 20751 | | 3.2 | |
| 2 | 1.994 | 32.4 | 70 | | | | | | | 1.2 | 1.2 | | 8745 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.599 | 1.7 | | 0.31 | | | | | | 3.2 | 5.8 | |
| 2 | 1.994 | 2.1 | | | | | | | | | | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | 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 | MOLECULAR REPLACEMENT | 1.599 | 27.413 | | | | 20751 | 1068 | 97.58 | | 0.1948 | 0.1937 | 0.19 | 0.218 | 0.22 | | |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.994 | 32.403 | | | | 8743 | 427 | 78.42 | | 0.2322 | 0.2303 | | 0.2707 | | | |
| 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] |
|---|
| | | | | |
| | | | | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| f_dihedral_angle_d | 19.963 |
| f_angle_d | 0.915 |
| f_bond_d | 0.092 |
| f_chiral_restr | 0.039 |
| f_plane_restr | 0.028 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1268 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 119 |
| Heterogen Atoms | 82 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| HKL-3000 | data processing |
| Coot | model building |
| PDB_EXTRACT | data extraction |
| Coot | model building |
| SCALA | data reduction |
| PHASER | phasing |
| SCALA | data scaling |
| LAUEGEN | data reduction |
