4TKM
Crystal structure of NADH-dependent reductase A1-R' complexed with NAD
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3AFM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | PEG 400, Ammonium sulphate, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, NAD |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.85 | 56.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 87.898 | α = 90 |
b = 87.898 | β = 90 |
c = 139.821 | γ = 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 | CCD | ADSC QUANTUM 315 | 2013-10-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL38B1 | 1.000 | SPring-8 | BL38B1 |
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 | 2.67 | 33.5 | 100 | 0.074 | 43.4 | 11.9 | 18404 | 38.3 |
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 | 2.67 | 2.77 | 99.9 | 0.306 | 9 | 12.2 |
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 | 3AFM | 2.67 | 33.45 | 17397 | 938 | 99.68 | 0.19916 | 0.19516 | 0.27801 | RANDOM | 49.85 |
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] | |
1.32 | 1.32 | 1.32 | -4.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.916 |
r_dihedral_angle_4_deg | 17.133 |
r_dihedral_angle_3_deg | 14.17 |
r_long_range_B_refined | 12.047 |
r_long_range_B_other | 12.046 |
r_dihedral_angle_1_deg | 6.632 |
r_scangle_other | 4.596 |
r_mcangle_it | 4.563 |
r_mcangle_other | 4.562 |
r_mcbond_it | 2.972 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3581 |
Nucleic Acid Atoms | |
Solvent Atoms | 81 |
Heterogen Atoms | 69 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data processing |
REFMAC | refinement |