Neutron crystal Structure of E.coli Dihydrofolate Reductase complexed with folate and NADP+ at pH4.5
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 | 4.5 | 291 | 40mg/mL DHFR-folate-NADP+ complex, 12% (v/v) PEG 400, 100mM MnCl2, 100mM NaAc, pH4.5 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.14 | 42.47 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 34.102 | α = 90 |
| b = 45.595 | β = 90 |
| c = 99.113 | 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 RAXIS IV++ | | 2014-08-10 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 291 | IMAGE PLATE | CUSTOM-MADE | | 2015-05-15 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 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 | 1.65 | 40 | 93.9 | 0.041 | | | | | | 24.94 | 3.9 | | 18163 | | | |
| 1 | 2.1 | 27.31 | 91.76 | 0.041 | | | | | | 25.3 | 2.3 | | 17681 | | | |
| 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 | 1.65 | 1.75 | | 0.426 | | | | | | 2.52 | 3.3 | |
| 2 | 2.1 | 2.18 | | 0.335 | | | | | | 2.3 | | |
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 | 1.65 | 27.31 | | 1.38 | | 17681 | 904 | 91.76 | | 0.1585 | 0.1571 | 0.16 | 0.1862 | 0.19 | | 26.3668 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.1 | 26.33 | | | | 7018 | 316 | 72.5 | | 0.1786 | 0.1766 | | 0.2187 | | | |
| 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] |
|---|
| | | | | |
| | | | | |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1268 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 346 |
| Heterogen Atoms | 129 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| PHASER | phasing |
