Perdeuterated E65Q-TIM complexed with PHOSPHOGLYCOLOHYDROXAMATE
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 2VXN | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | | 293.15 | 0.1 M sodium acetate, 1 mM Na EDTA, 1 mM DTT,18% PEG6000 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.47 | 50.16 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 98.323 | α = 90 |
| b = 52.678 | β = 117.86 |
| c = 58.665 | γ = 90 |
| Symmetry |
|---|
| Space Group | C 1 2 1 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 293 | PIXEL | DECTRIS PILATUS3 6M | | 2016-11-01 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | IMAGE PLATE | CUSTOM-MADE | | 2018-03-28 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 0.89 | PETRA III, EMBL c/o DESY | P14 (MX2) |
| 2 | NUCLEAR REACTOR | ILL BEAMLINE LADI III | 2.7-3.5 | ILL | LADI III |
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 | 1.1 | 45.01 | 96 | | | 0.043 | | 0.999 | | 14.77 | 3.2 | | 104600 | | | |
| 2 | 1.8 | 40 | 78 | | | 0.194 | | 0.955 | | 3.8 | 5.2 | | 19145 | | | |
| 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 | 1.1 | 1.16 | | | | 0.96 | | 0.663 | | 2.1 | | |
| 2 | 1.8 | 1.9 | | | | 0.514 | | 0.666 | | 2.5 | | |
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 | 1.1 | 45.01 | | 1.35 | | 104575 | 5194 | 96.17 | | 0.1444 | 0.1437 | 0.14 | 0.1576 | 0.16 | | 23.4706 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.8 | 30.5502 | | | | 19144 | 965 | 77.37 | | 0.222 | 0.2201 | | 0.2593 | | | |
| 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 | 19.626 |
| f_angle_d | 1.393 |
| f_chiral_restr | 0.099 |
| f_bond_d | 0.01 |
| f_plane_restr | 0.008 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1871 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 381 |
| Heterogen Atoms | 14 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| XDS | data reduction |
| LAUEGEN | data reduction |
| XSCALE | data scaling |
| SCALA | data scaling |
| PHASER | phasing |
