7LNU
Ternary complex of the Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus bound to isopentenyl monophosphate and ATP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7LNV | cma apo model |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 275 | 0.1 M Bis-Tris, pH 5.5 28% PEG 3350 0.1 M Sodium Chloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.892 | α = 90 |
b = 74.503 | β = 90 |
c = 171.691 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 200K | Osmic Veri Max Mirrors | 2016-07-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54178 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.5 | 50 | 91 | 0.1 | 0.047 | 0.991 | 11.9 | 4.2 | 18714 | 30.42 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.5 | 2.54 | 0.681 | 0.394 | 0.65 | 1.93 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | cma apo model | 2.5 | 45.39 | 1.33 | 18357 | 937 | 97.1 | 0.2324 | 0.2294 | 0.2868 | 32.43 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 23.2858 |
f_angle_d | 0.6516 |
f_chiral_restr | 0.0454 |
f_plane_restr | 0.0028 |
f_bond_d | 0.0021 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3808 |
Nucleic Acid Atoms | |
Solvent Atoms | 164 |
Heterogen Atoms | 119 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-3000 | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |