6C07
Crystal Structure of S-Adenosylmethionine synthetase (MetK/Mat) from Cryptosporidium parvum
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 25% PEG3350, 0.2 M ammonium sulfate, 0.01 M magnesium chloride, 0.1 M Bis-Tris, pH 6.5 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.23 | 44.73 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 134.39 | α = 90 |
b = 62.06 | β = 90.65 |
c = 191.583 | γ = 90 |
Symmetry | |
---|---|
Space Group | I 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 | 100 | PIXEL | DECTRIS EIGER X 16M | 2016-12-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 1.03315 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.85 | 59.05 | 98.7 | 0.05477 | 0.07745 | 0.05477 | 0.996 | 8.15 | 2.7 | 185005 | 25.34 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.85 | 1.916 | 94.92 | 0.5238 | 0.7408 | 0.5238 | 0.532 | 1.39 | 1.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 4ODJ | 1.85 | 19.988 | 1.34 | 127368 | 6388 | 94.37 | 0.1596 | 0.1573 | 0.2036 | RANDOM |
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 | 11.676 |
f_angle_d | 1.09 |
f_chiral_restr | 0.063 |
f_bond_d | 0.011 |
f_plane_restr | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 11337 |
Nucleic Acid Atoms | |
Solvent Atoms | 1201 |
Heterogen Atoms | 10 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
MOSFLM | data reduction |
Aimless | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |