1G5H
CRYSTAL STRUCTURE OF THE ACCESSORY SUBUNIT OF MURINE MITOCHONDRIAL POLYMERASE GAMMA
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | Sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 41.94 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96.623 | α = 90 |
b = 133.422 | β = 90 |
c = 135.038 | 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 | CUSTOM-MADE | 2000-07-10 | M | MAD | ||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 4 | 2000-06-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | NSLS | X25 | |
2 | SYNCHROTRON | NSLS BEAMLINE X26C | 1.1 | NSLS | X26C |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | ||||||||
1,2 | 1.95 | 20 | 99.96 | 0.072 | 29.6 | 7.4 | 127289 | 127238 | -3 | -3 | 30.741 |
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) | |||||||||||
1,2 | 1.95 | 2.05 | 100 | 0.5 | 2.2 | 3.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | 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 | MAD | THROUGHOUT | 1.95 | 20 | -1000 | 124693 | 124642 | 2545 | 100 | 0.183 | 0.183 | 0.224 | RANDOM | 42.48 |
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] | |
-0.02 | 0.02 | 0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_multtor_nbd | 18.32 |
p_scangle_it | 13.076 |
p_scbond_it | 9.644 |
p_mcangle_it | 7.234 |
p_mcbond_it | 4.756 |
p_singtor_nbd | 4.341 |
p_angle_deg | 1.714 |
p_chiral_restr | 0.11 |
p_bond_d | 0.017 |
p_plane_restr | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12891 |
Nucleic Acid Atoms | |
Solvent Atoms | 872 |
Heterogen Atoms | 16 |
Software
Software | |
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Software Name | Purpose |
SHAKE | model building |
SnB | phasing |
SOLVE | phasing |
SHARP | phasing |
REFMAC | refinement |
MARMAD | data reduction |
DENZO | data reduction |
SCALEPACK | data scaling |