3CMC
Thioacylenzyme intermediate of Bacillus stearothermophilus phosphorylating GAPDH
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.9 | 293 | 2.7 M Ammonium Sulfate, 100 mM Tris-HCl buffer pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.65 | 53.65 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.67 | α = 90 |
b = 122.63 | β = 111.12 |
c = 81.79 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MAR CCD 165 mm | 2006-02-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | 0.806 | EMBL/DESY, HAMBURG | X13 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.77 | 29.5 | 98.7 | 0.028 | 32.1 | 3.7 | 142733 | 142733 | 23.6 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.77 | 1.88 | 92.9 | 0.189 | 6.5 | 3.2 | 20259 |
Refinement
Statistics | |||||||||||||||||||
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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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.77 | 29.5 | 149866 | 142733 | 7133 | 97.68 | 0.163 | 0.163 | 0.161 | 0.198 | RANDOM | 25.69 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.3 | -2.185 | -1.163 | 0.863 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
IMPROPER ANGLES (DEGREES) | 25.962 |
t_dihedral_angle_d | 16.964 |
t_it | 1.686 |
t_angle_deg | 1.266 |
t_nbd | 0.056 |
t_gen_planes | 0.02 |
t_bond_d | 0.011 |
t_trig_c_planes | 0.011 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10100 |
Nucleic Acid Atoms | |
Solvent Atoms | 1740 |
Heterogen Atoms | 358 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
MOLREP | phasing |
TNT | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
XDS | data reduction |
BUSTER-TNT | refinement |