2QD0
Crystal structure of mitoNEET
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | 100 mM Tris-HCl, 18% PEG 3350 , 200 mM KI., pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
2 | VAPOR DIFFUSION, HANGING DROP | 7.4 | 293 | 100 mM Tris-HCl, 30% PEG 2000 ,100 mM NaCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.838 | α = 90 |
b = 59.139 | β = 90 |
c = 65.971 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | mirrors | 2006-05-19 | M | SINGLE WAVELENGTH | |||||
2 | 2 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2006-07-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.5418 | ||
2 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1.0 | SPring-8 | BL41XU |
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 | 1.8 | 50 | 95.2 | 0.045 | 15.2 | 6.4 | 15523 | -3 |
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) | |||||||||||
1,2 | 1.8 | 1.83 | 76.8 | 0.216 | 5.4 | 616 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.81 | 21.92 | 14902 | 739 | 91.62 | 0.166 | 0.164 | 0.193 | RANDOM | 49.944 |
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] | |
5.12 | -3.93 | -1.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 24.065 |
r_dihedral_angle_3_deg | 14.192 |
r_dihedral_angle_4_deg | 6.664 |
r_dihedral_angle_1_deg | 5.679 |
r_scangle_it | 2.877 |
r_scbond_it | 1.939 |
r_angle_refined_deg | 1.888 |
r_mcangle_it | 1.214 |
r_mcbond_it | 0.803 |
r_nbtor_refined | 0.311 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1074 |
Nucleic Acid Atoms | |
Solvent Atoms | 95 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALEPACK | data scaling |
CNS | phasing |
CNS | refinement |
DENZO | data reduction |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |