1XGV
Isocitrate Dehydrogenase from the hyperthermophile Aeropyrum pernix
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 291 | PEG 6K, Magnesium chloride, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.6 | 52 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 107.569 | α = 90 |
b = 107.569 | β = 90 |
c = 171.143 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 43 21 2 |
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 | MARRESEARCH | 2003-05-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I711 | 0.9089 | MAX II | I711 |
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 | 39.84 | 0.055 | 17.97 | 4.7 | 51805 | 51735 | 1.35 | 2 |
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 | 2.2 | 2.24 | 100 | 0.497 | 2.91 | 4 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3ICD | 2.2 | 39.84 | 51590 | 48984 | 2606 | 99.87 | 0.22609 | 0.22479 | 0.25059 | RANDOM | 19.407 |
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] | |
-0.65 | -0.65 | 1.3 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 5.575 |
r_scangle_it | 2.427 |
r_scbond_it | 1.553 |
r_angle_refined_deg | 1.272 |
r_mcangle_it | 0.761 |
r_mcbond_it | 0.415 |
r_symmetry_vdw_refined | 0.227 |
r_nbd_refined | 0.205 |
r_symmetry_hbond_refined | 0.192 |
r_xyhbond_nbd_refined | 0.147 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6595 |
Nucleic Acid Atoms | |
Solvent Atoms | 162 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |