X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | Other | MR was performed using a preliminary DMO structure. This early DMO structure was obtained largely using a high-redundancy, 1.5418 A wavelength data set for Fe single wavelength anomalous dispersion (SAD) phasing, with assistance from the sulfur anomalous signal in a high-redundancy, 2.29 A wavelength data set. | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 294 | The purified protein was concentrated to 10-20 mg/ml and buffer exchanged into 25 mM Tris-HCl, pH 8.0, 30-50 mM NaCl, 25 mM sodium citrate. DMO crystals were grown using the vapor diffusion by sitting drop method, with a reservoir solution of 8-11% PEG 6000, 100 mM sodium acetate buffer-pH 5.5, 1 M LiCl, and 4ul droplets of varying protein-to-precipitant ratios. To prepare a DMO-non-heme iron-dicamba crystal, some crystals were transferred to a cryo-amenable storage solution that contained 25 mM dicamba (12.3 % PEG6000, 95 mM sodium acetate pH 5.5, 21% glycerol, 1mM NaN3, and 25 mM dicamba) for 5-6 hours prior to plunge-cooling for cryo-storage and low temperature data collection. VAPOR DIFFUSION, SITTING DROP, temperature 294K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.59 | 52.52 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 80.8 | α = 90 |
| b = 80.8 | β = 90 |
| c = 159.6 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 32 |
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 | MARMOSAIC 300 mm CCD | 2005-06-30 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.000 | APS | 22-ID |
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 | 2.2 | 36.04 | 99.7 | 0.056 | 27.6 | 4 | 59051 | 58874 | |||||||||||
| 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) | |||||||||||
| 2.2 | 2.28 | 100 | 0.419 | 4 | |||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | THROUGHOUT | MR was performed using a preliminary DMO structure. This early DMO structure was obtained largely using a high-redundancy, 1.5418 A wavelength data set for Fe single wavelength anomalous dispersion (SAD) phasing, with assistance from the sulfur anomalous signal in a high-redundancy, 2.29 A wavelength data set. | 2.2 | 20 | 50201 | 5057 | 84.9 | 0.23 | 0.21 | 0.266 | 0.23 | random | 47.933 | ||||||
| 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] | |
| -0.098 | -0.04 | -0.098 | 0.196 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_scangle_it | 2.618 |
| c_mcangle_it | 2.146 |
| c_scbond_it | 1.81 |
| c_angle_deg | 1.32 |
| c_mcbond_it | 1.302 |
| c_bond_d | 0.006 |
| c_bond_d_na | |
| c_bond_d_prot | |
| c_angle_d | |
| c_angle_d_na | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 7809 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 483 |
| Heterogen Atoms | 40 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SERGUI | data collection |
| PHASER | phasing |
| CNX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |














