3KD8
Cofactor-Independent Phosphoglycerate mutase from Thermoplasma Acidophilum DSM 1728
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 296 | 0.16M magnesium chloride 0.08M tris HCl, pH 8.5 24% PEG 4000 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 87.911 | α = 90 |
b = 137.081 | β = 90 |
c = 67.088 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 QUANTUM 210r | double-crystal monochromator Si(111) | 2009-08-18 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.97880, 0.97904 | APS | 19-BM |
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 | 2.6 | 73.92 | 99.84 | 0.105 | 30.75 | 9.5 | 25760 | 3 |
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) | |||||||||||
2.6 | 2.62 | 99.5 | 0.509 | 2.923 | 4.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | MAD | THROUGHOUT | 2.6 | 73.92 | 24352 | 1305 | 99.81 | 0.21145 | 0.20737 | 0.28782 | RANDOM | 33.771 |
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] | |
0.16 | -2.3 | 2.14 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.939 |
r_dihedral_angle_3_deg | 20.488 |
r_dihedral_angle_4_deg | 20.357 |
r_dihedral_angle_1_deg | 7.276 |
r_scangle_it | 4.004 |
r_scbond_it | 2.447 |
r_angle_refined_deg | 1.643 |
r_mcangle_it | 1.524 |
r_mcbond_it | 0.786 |
r_chiral_restr | 0.114 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5616 |
Nucleic Acid Atoms | |
Solvent Atoms | 145 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SBC-Collect | data collection |
MLPHARE | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |