4XW4
X-ray structure of PKAc with AMPPNP, SP20, calcium ions
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 100 mM MES pH 6.5, 5 mM DTT, 15-20% PEG 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 52.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.364 | α = 90 |
b = 78.816 | β = 90 |
c = 97.985 | 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 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2013-11-13 | 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) | 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 | 1.82 | 40 | 97.8 | 0.036 | 33.08 | 3.8 | 36595 |
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) | |||||||||||
1.82 | 1.89 | 94.4 | 0.467 | 2.2 | 3.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | FREE R-VALUE | 1.82 | 20 | 36595 | 36595 | 1832 | 91.9 | 0.1835 | 0.184 | 0.2397 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
2 | 3297 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_anti_bump_dis_restr | 0.095 |
s_similar_adp_cmpnt | 0.08 |
s_non_zero_chiral_vol | 0.066 |
s_zero_chiral_vol | 0.051 |
s_angle_d | 0.027 |
s_from_restr_planes | 0.0235 |
s_bond_d | 0.011 |
s_similar_dist | |
s_rigid_bond_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2917 |
Nucleic Acid Atoms | |
Solvent Atoms | 343 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
SHELX | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
SHELX | phasing |
SHELXL-97 | refinement |