2XW6
The Crystal Structure of Methylglyoxal Synthase from Thermus sp. GH5 Bound to Phosphate Ion.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 8 | 277 | CRYSTALS WERE OBTAINED USING MICROBATCH METHOD AT 4C. CRYSTALLIZATION DROPS WERE MADE BY MIXING 2 MICROLITER OF A 7.8 MG/ML PROTEIN SOLUTION IN 50 MM TRIS-HCL, 300 MM NACL, 160 MM IMIDAZOLE AND 20% GLYCEROL WITH EQUAL AMOUNT OF CRYSTALLIZATION SOLUTION CONTAINING 0.1 M TRIS-HCL (PH 8.0), 29% W/V POLYETHYLENE GLYCOL (PEG) 4000. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 43.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.636 | α = 90 |
b = 115.172 | β = 90 |
c = 120.431 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | ADSC CCD | MIRRORS | 2009-03-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | SOLEIL | PROXIMA 1 |
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 | 1.08 | 42.2 | 96.6 | 0.05 | 12 | 3.6 | 156269 |
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 | 1.08 | 1.12 | 81.1 | 0.54 | 1.8 | 2.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | FREE R-VALUE | PDB ENTRY 1WO8 | 1.08 | 42.2 | 148053 | 7806 | 96.6 | 0.129 | 0.129 | 0.161 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
58 | 2925.64 | 3293.85 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.109 |
s_non_zero_chiral_vol | 0.093 |
s_zero_chiral_vol | 0.092 |
s_anti_bump_dis_restr | 0.083 |
s_similar_adp_cmpnt | 0.051 |
s_angle_d | 0.034 |
s_from_restr_planes | 0.03 |
s_bond_d | 0.015 |
s_rigid_bond_adp_cmpnt | 0.006 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2903 |
Nucleic Acid Atoms | |
Solvent Atoms | 463 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
SHELXL-97 | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |