3GBT
Crystal structure of gluconate kinase from Lactobacillus acidophilus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 291 | 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 35% v/v tert-Butanol, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.82 | 67.79 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 122.638 | α = 90 |
b = 96.008 | β = 93.32 |
c = 72.94 | γ = 90 |
Symmetry | |
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Space Group | C 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 | 110 | CCD | ADSC QUANTUM 210 | mirrors | 2009-02-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X12C | 0.9792 | NSLS | X12C |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.4 | 50 | 97.1 | 0.146 | 11.2 | 5.8 | 33281 | 33170 | 34.76 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.4 | 2.53 | 88.3 | 0.606 | 1.7 | 4.5 | 4255 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution 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 | SAD | 2.4 | 40.079 | 33170 | 32163 | 1638 | 97.18 | 0.2009 | 0.1992 | 0.2306 | Random | 34.76 |
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] | |
-3.9761 | -3.7951 | 11.2437 | -7.2677 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_bond_d | |
f_bond_d_na | |
f_bond_d_prot | |
f_angle_d | |
f_angle_d_na | |
f_angle_d_prot | |
f_angle_deg | |
f_angle_deg_na | |
f_angle_deg_prot | |
f_dihedral_angle_d |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3801 |
Nucleic Acid Atoms | |
Solvent Atoms | 131 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
CBASS | data collection |
PHENIX | model building |
PHENIX | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHENIX | phasing |