1ZPT
Escherichia coli Methylenetetrahydrofolate Reductase (reduced) complexed with NADH, pH 7.25
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1B5T | PDB entry 1B5T |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.25 | 295 | PEG 4000, LITHIUM SULFATE, SODIUM CACODYLATE, ETHANOL, MESO-ERYTHRITOL, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.69 | 54.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 103.613 | α = 90 |
b = 127.735 | β = 121.73 |
c = 97.831 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | IMAGE PLATE | RIGAKU | 2003-09-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.95 | 19.9 | 97.9 | 0.038 | 19.4 | 3 | 78597 | 76927 | 21 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.95 | 2.02 | 96.4 | 0.312 | 3.75 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1B5T | 1.95 | 19.9 | 78597 | 76927 | 3876 | 97.9 | 0.219 | 0.219 | 0.246 | RANDOM | 33.8 |
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] | |
1.31 | -2.75 | 0.84 | -2.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.3 |
c_scangle_it | 2.39 |
c_mcangle_it | 1.63 |
c_scbond_it | 1.58 |
c_angle_deg | 1.4 |
c_mcbond_it | 1.02 |
c_improper_angle_d | 0.85 |
c_bond_d | 0.008 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6316 |
Nucleic Acid Atoms | |
Solvent Atoms | 326 |
Heterogen Atoms | 311 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
SCALEPACK | data scaling |
EPMR | phasing |