8X4I
Crystal structure of the D117A mutant of DIMT1 in complex with 5'-methylthioadenosine from Pyrococcus horikoshii
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8X3W |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 6.4 | 293 | 0.2 M Zinc Acetate Dihydrate, 20% (w/v) PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 46.98 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 124.92 | α = 90 |
b = 124.92 | β = 90 |
c = 36.81 | γ = 120 |
Symmetry | |
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Space Group | P 6 |
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 RAXIS IV++ | VariMax HF | 2022-09-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 3.3 | 62.54 | 93.2 | 0.164 | 0.188 | 0.091 | 0.967 | 9.1 | 4.3 | 9013 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 3.3 | 3.57 | 87.2 | 0.513 | 0.586 | 0.281 | 0.875 | 4.3 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 3.3 | 62.54 | 4330 | 448 | 92.56 | 0.20993 | 0.20102 | 0.28654 | RANDOM | 128.649 |
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] | |
-1.5 | -0.75 | -1.5 | 4.85 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 17.478 |
r_long_range_B_refined | 14.003 |
r_long_range_B_other | 14.001 |
r_dihedral_angle_1_deg | 9.511 |
r_mcangle_it | 8.928 |
r_mcangle_other | 8.925 |
r_scangle_other | 8.465 |
r_dihedral_angle_2_deg | 6.044 |
r_mcbond_it | 5.395 |
r_mcbond_other | 5.395 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2186 |
Nucleic Acid Atoms | |
Solvent Atoms | 6 |
Heterogen Atoms | 21 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
MOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |
REFMAC | refinement |
Coot | model building |
PDB_EXTRACT | data extraction |