4GNJ
Crystal Structure Analysis of Leishmania siamensis Triosephosphate Isomerase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 6.5 | 291 | 0.20M calcium acetate, 0.10M sodium cacodylate trihydrate, 18% PEG 8000, pH 6.5, MICROBATCH, temperature 291K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.18 | 43.45 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 39.58 | α = 90 |
b = 78.79 | β = 101.15 |
c = 83.16 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 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 | CCD | RAYONIX SX-165mm | HELIOS | 2011-03-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.5418 |
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 | 1.93 | 81.6 | 93.7 | 0.054 | 0.202 | 14.2 | 3.3 | 35257 | 2 | 2 | 16.4 |
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 | 1.93 | 2.03 | 90.2 | 0.202 | 0.202 | 3.8 | 3.1 | 15450 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1AMK | 1.93 | 21.61 | 2 | 2 | 33449 | 1793 | 93.23 | 0.15373 | 0.15373 | 0.15132 | 0.19932 | RANDOM | 15.209 |
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 | 0.29 | 0.52 | -0.62 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.698 |
r_dihedral_angle_4_deg | 17.724 |
r_dihedral_angle_3_deg | 12.958 |
r_dihedral_angle_1_deg | 6.083 |
r_scangle_it | 3.021 |
r_scbond_it | 1.837 |
r_angle_refined_deg | 1.358 |
r_mcangle_it | 0.982 |
r_mcbond_it | 0.56 |
r_chiral_restr | 0.091 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3749 |
Nucleic Acid Atoms | |
Solvent Atoms | 365 |
Heterogen Atoms | 3 |
Software
Software | |
---|---|
Software Name | Purpose |
MAR345 | data collection |
MOLREP | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |