5YOH
Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105M mutant) in complex with Methionine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1YJ3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 0.1M Hepes, 27% Peg3350, 3% glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.95 | 36.86 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.332 | α = 90 |
b = 48.69 | β = 95.3 |
c = 56.151 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 RAXIS IV++ | 2016-05-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 |
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 | 1.62 | 28.59 | 92.2 | 0.027 | 0.038 | 0.026 | 0.998 | 59.8 | 1.9 | 32311 | 21.95 |
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 | 1.62 | 1.68 | 78.1 | 0.118 | 0.166 | 0.117 | 0.961 | 1.9 |
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 | 1YJ3 | 1.63 | 28.59 | 32306 | 1526 | 96.89 | 0.1683 | 0.166 | 0.218 | RANDOM | 23.683 |
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 |
r_dihedral_angle_2_deg | 39.804 |
r_dihedral_angle_4_deg | 21.046 |
r_dihedral_angle_3_deg | 12.756 |
r_dihedral_angle_1_deg | 6.198 |
r_angle_refined_deg | 2.159 |
r_angle_other_deg | 1.094 |
r_chiral_restr | 0.132 |
r_bond_refined_d | 0.022 |
r_gen_planes_refined | 0.012 |
r_gen_planes_other | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2154 |
Nucleic Acid Atoms | |
Solvent Atoms | 208 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
MOLREP | model building |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
HKL-2000 | data collection |
HKL-2000 | phasing |