5O6H
Human NMT1 in complex with myristoyl-CoA and inhibitor IMP-917
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4C2Y |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 291 | 0.4M Sodium phosphate buffer, 17.5% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.28 | 45.95 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 79.138 | ¦Á = 90 |
b = 178.852 | ¦Â = 90 |
c = 58.465 | ¦Ã = 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 | PIXEL | DECTRIS PILATUS 2M | 2013-05-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.9200 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.29 | 89 | 99.1 | 0.062 | 0.039 | 0.999 | 14.7 | 6.2 | 206823 | 9.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.29 | 1.31 | 93.1 | 0.651 | 0.595 | 0.697 | 1.6 | 3.4 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 4c2y | 1.29 | 55 | 195765 | 10300 | 98.68 | 0.16533 | 0.16384 | 0.19348 | RANDOM | 17.134 |
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] | |
1.7 | -0.57 | -1.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.518 |
r_dihedral_angle_4_deg | 18.794 |
r_dihedral_angle_3_deg | 14.05 |
r_dihedral_angle_1_deg | 6.437 |
r_long_range_B_refined | 5.269 |
r_scbond_it | 2.823 |
r_angle_refined_deg | 2.498 |
r_mcangle_it | 2.483 |
r_mcbond_it | 1.685 |
r_chiral_restr | 0.175 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6272 |
Nucleic Acid Atoms | |
Solvent Atoms | 1018 |
Heterogen Atoms | 252 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
REFMAC | phasing |