4Z9M
Crystal structure of human sarcomeric mitochondrial creatine kinase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 291 | 17% PEG-3350, 10mM DTT, 0.2M diammonium citrate, 0.1M Bis-TRIS, protein buffer also contained magnesium chloride, creatine, ADP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.78 | 55.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 93.057 | α = 70.12 |
b = 106.058 | β = 84.57 |
c = 114.932 | γ = 68.61 |
Symmetry | |
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Space Group | P 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 | CCD | ADSC QUANTUM 210 | 2006-02-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.00003 | APS | 17-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 49.09 | 95.4 | 0.077 | 0.077 | 0.995 | 8.5 | 2 | 247985 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2 | 2.03 | 95.5 | 0.897 | 0.894 | 0.318 | 1 | 2 | 12346 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | THROUGHOUT | 2GL6 | 2.1 | 40 | 214294 | 4357 | 95.4 | 0.203 | 0.2023 | 0.2362 | THIN SHELLS (SFTOOLS) | 38.291 |
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] | |
-0.6 | 0.37 | -0.84 | -0.14 | -0.49 | 0.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.673 |
r_dihedral_angle_4_deg | 16.369 |
r_dihedral_angle_3_deg | 12.095 |
r_dihedral_angle_1_deg | 5.749 |
r_mcangle_it | 3.829 |
r_mcbond_it | 2.49 |
r_mcbond_other | 2.49 |
r_angle_refined_deg | 1.267 |
r_angle_other_deg | 0.903 |
r_chiral_restr | 0.069 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 21843 |
Nucleic Acid Atoms | |
Solvent Atoms | 849 |
Heterogen Atoms | 306 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data scaling |