5G41
Crystal structure of adenylate kinase ancestor 4 with Zn, Mg and Ap5A bound
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 291 | 0.5 UL OF PROTEIN MIXTURE (20 MG/ML ADK ANCESTOR 4 AND 10 MM MGAP5A IN 40 MM MOPS PH 7.0, 50 MM NACL, 2 MM TCEP) WAS MIXED WITH 0.5 UL OF MOTHER LIQUOR (100 MM SODIUM ACETATE PH 4.6, 50 MM MGCL2, 2M AMMONIUM SULFATE). CRYSTALS WERE GROWN BY SITTING DROP METHOD AT 18C. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.77 | 55.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.999 | α = 90 |
b = 73.999 | β = 90 |
c = 100.782 | γ = 90 |
Symmetry | |
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Space Group | P 43 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 | CCD | ADSC CCD | 2014-07-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | ALS | 8.2.1 |
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 | 1.54 | 59.65 | 88.1 | 0.06 | 23.8 | 13.1 | 37185 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.54 | 1.57 | 97.1 | 1.12 | 2 | 9.5 |
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 | PDB ENTRY 1P3J | 1.54 | 59.65 | 36242 | 866 | 88.02 | 0.15462 | 0.15356 | 0.1963 | RANDOM | 26.5 |
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] | |
0.12 | 0.12 | -0.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 44.652 |
r_dihedral_angle_2_deg | 35.078 |
r_sphericity_bonded | 26.59 |
r_dihedral_angle_3_deg | 13.5 |
r_dihedral_angle_4_deg | 10.699 |
r_dihedral_angle_1_deg | 5.607 |
r_mcangle_it | 3.13 |
r_scbond_it | 2.863 |
r_mcbond_it | 2.404 |
r_mcbond_other | 2.387 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1657 |
Nucleic Acid Atoms | |
Solvent Atoms | 185 |
Heterogen Atoms | 59 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |