2ELD
Mutant L160M structure of PH0725 from Pyrococcus horikoshii OT3
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1WNG | pDB entry 1WNG |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | Microbach | 5.5 | 295 | 3.85M Na Formic acid, 0.1M Acetic acid, pH 5.5, Microbach, temperature 295K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.28 | 62.45 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 105.133 | α = 90 |
b = 105.133 | β = 90 |
c = 140.553 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 41 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 | RIGAKU JUPITER | mirror | 2006-11-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B1 | 1.0 | SPring-8 | BL26B1 |
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 | 2.3 | 30 | 100 | 0.073 | 0.073 | 5.7 | 13.9 | 35651 | 35651 | 39.2 |
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 | 2.3 | 2.38 | 100 | 0.277 | 0.272 | 3.3 | 14.4 |
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 1WNG | 2.3 | 30 | 35651 | 35651 | 1777 | 100 | 0.204 | 0.204 | 0.235 | RANDOM | 45.9 |
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] | |
0.82 | 0.82 | -1.63 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.9 |
c_scangle_it | 3.22 |
c_mcangle_it | 2.39 |
c_scbond_it | 2.16 |
c_mcbond_it | 1.45 |
c_angle_deg | 1.3 |
c_improper_angle_d | 0.78 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4172 |
Nucleic Acid Atoms | |
Solvent Atoms | 307 |
Heterogen Atoms | 33 |
Software
Software | |
---|---|
Software Name | Purpose |
CNS | refinement |
CrystalClear | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |