3E7F
Crystal structure of 6-phosphogluconolactonase from Trypanosoma brucei complexed with 6-phosphogluconic acid
X-RAY DIFFRACTION
Crystallization
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.44 | 49.65 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 49.66 | α = 90 |
b = 87 | β = 96.43 |
c = 64.91 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 110 | CCD | ADSC QUANTUM 4 | 2006-10-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-3 | 0.931 | ESRF | ID14-3 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.2 | 24 | 99.3 | 27717 | 27717 | 1 | 1 | 34.013 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
2.2 | 2.5 | 86.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | THROUGHOUT | 2.2 | 23.96 | 27716 | 27717 | 1393 | 99.17 | 0.1776 | 0.1738 | 0.2493 | RANDOM | 33.21 |
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] | |
-6.19098368 | -3.92252768 | 7.60675712 | -1.41577344 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_dihedral_angle_d | 20.359 |
t_it | 1.692 |
t_angle_deg | 1.302 |
t_nbd | 0.051 |
t_gen_planes | 0.017 |
t_bond_d | 0.011 |
t_trig_c_planes | 0.011 |
t_incorr_chiral_ct | |
t_pseud_angle |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3937 |
Nucleic Acid Atoms | |
Solvent Atoms | 431 |
Heterogen Atoms | 36 |
Software
Software | |
---|---|
Software Name | Purpose |
BUSTER-TNT | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |
REFMAC | refinement |