4TYZ
Crystal structure of the C-terminal domain of an unknown protein from Leishmania infantum
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9 | 290 | Reagents JCSG+ sceen b3: 20% PEG 6000, 100mM Bicine pH 9.0; LeinA.18749.a.B1.PS02018 at 8.28mg/ml |
2 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | RigakuReagents JCSG+ sceen a9: 20% PEG 3350, 200mM Ammonium chloride; LeinA.18749.a.B1.PS02018 at 8.28mg/ml; the crystal was soaked for 10sec each in reservoir solution with 10% EG/500mM NaI, 20% EG/1000mM NaI, this sample was used for in-house phasing |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.68 | 54 |
2.68 | 54 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 58.86 | α = 90 |
b = 58.86 | β = 90 |
c = 135.12 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 31 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 | CCD | RAYONIX MX-225 | 2014-06-13 | M | SINGLE WAVELENGTH | ||||||
2 | 2 | x-ray | 100 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
2 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | 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 | 1.6 | 50 | 99.4 | 0.048 | 0.048 | 0.052 | 30.88 | 7.3 | 36702 | 36500 | -3 | 13.71 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.6 | 1.64 | 100 | 0.522 | 0.562 | 3.73 | 7.29 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | FREE R-VALUE | 1.6 | 33.752 | 1.36 | 36479 | 1909 | 99.57 | 0.16 | 0.1585 | 0.1862 | Random selection | 19.8652 |
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 | 13.559 |
f_angle_d | 1.022 |
f_chiral_restr | 0.042 |
f_bond_d | 0.007 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1743 |
Nucleic Acid Atoms | |
Solvent Atoms | 296 |
Heterogen Atoms | 4 |
Software
Software | |
---|---|
Software Name | Purpose |
XDS | data scaling |
XSCALE | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
ARP | model building |
PHENIX | refinement |
CNS | refinement |