5G3Y
Crystal structure of adenylate kinase ancestor 1 with Zn and ADP 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 1 AND 20 MM MGADP 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 |
2.09 | 41.29 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.917 | α = 90 |
b = 63.341 | β = 90 |
c = 70.457 | 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 | CCD | ADSC QUANTUM 315 | 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 | 1.18 | 47.1 | 96.7 | 0.06 | 15.8 | 6.2 | 67513 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.18 | 1.2 | 85 | 0.45 | 2 | 2.7 |
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 | 1.18 | 37.7 | 66341 | 1033 | 96.42 | 0.13234 | 0.13205 | 0.14992 | RANDOM | 15.493 |
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] | |
-0.14 | -0.03 | 0.17 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.322 |
r_sphericity_free | 26.444 |
r_dihedral_angle_4_deg | 15.623 |
r_dihedral_angle_3_deg | 10.551 |
r_sphericity_bonded | 9.192 |
r_dihedral_angle_1_deg | 5.038 |
r_scbond_it | 1.676 |
r_angle_refined_deg | 1.65 |
r_mcangle_it | 1.449 |
r_rigid_bond_restr | 1.326 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1647 |
Nucleic Acid Atoms | |
Solvent Atoms | 261 |
Heterogen Atoms | 55 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |