1GUY
Structural Basis for Thermophilic Protein Stability: Structures of Thermophilic and Mesophilic Malate Dehydrogenases
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1LDB | MODIFICATION OF PDB ENTRY 1LDB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.6 | 5-15% PEG400, 100 MM NAAC, PH 4.6, 40MM 5-15% PEG400, 100 MM NAAC, PH 4.6, 40MM CDAC |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 51 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 106.67 | ¦Á = 90 |
b = 106.67 | ¦Â = 90 |
c = 103.99 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 31 2 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 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7B | EMBL/DESY, HAMBURG | BW7B |
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 | 2.2 | 25 | 99.7 | 0.124 | 2.5 | 35062 | 9.8 |
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 | 2.2 | 2.33 | 87.1 | 0.284 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | MODIFICATION OF PDB ENTRY 1LDB | 2.2 | 19.87 | 35062 | 1083 | 99.9 | 0.174 | 0.174 | 0.197 | RANDOM | 20.8 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.3 |
c_scangle_it | 3.33 |
c_scbond_it | 2.3 |
c_mcangle_it | 1.93 |
c_mcbond_it | 1.27 |
c_angle_deg | 1.1 |
c_improper_angle_d | 0.78 |
c_bond_d | 0.005 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4418 |
Nucleic Acid Atoms | |
Solvent Atoms | 315 |
Heterogen Atoms | 93 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
AMoRE | phasing |