2RAQ
Crystal structure of the MTH889 protein from Methanothermobacter thermautotrophicus. Northeast Structural Genomics Consortium target TT205
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | MICROBATCH UNDER OIL | 7.5 | 291 | Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM DTT. Reservoir solution: 100 mM HEPES pH 7.5, 18% PEG 400, 200 mM CaCl2, 3% 1,6-Hexanediol, MICROBATCH UNDER OIL, temperature 291K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.41 | 48.88 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 113.569 | α = 90 |
b = 113.569 | β = 90 |
c = 114.53 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 42 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 | ADSC QUANTUM 4 | mirrors | 2007-06-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4A | 0.97900 | NSLS | X4A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 3.1 | 80.58 | 99.5 | 0.085 | 0.068 | 26.13 | 7.3 | 25673 | 25673 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.1 | 3.21 | 99.8 | 0.313 | 0.282 | 6.13 | 6.7 | 2573 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 3.11 | 80.58 | 2 | 25802 | 13283 | 691 | 99.4 | 0.22 | 0.21871 | 0.21559 | 0.2802 | RANDOM | 55.914 |
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] | |
0.1 | 0.1 | -0.2 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 43.678 |
r_dihedral_angle_3_deg | 24.829 |
r_dihedral_angle_4_deg | 20.343 |
r_dihedral_angle_1_deg | 7.979 |
r_scangle_it | 3.349 |
r_scbond_it | 2.258 |
r_angle_refined_deg | 1.774 |
r_mcangle_it | 1.255 |
r_mcbond_it | 0.694 |
r_nbtor_refined | 0.336 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5082 |
Nucleic Acid Atoms | |
Solvent Atoms | 54 |
Heterogen Atoms | 14 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
ADSC | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
SnB | phasing |
RESOLVE | phasing |