2JDI
Ground state structure of F1-ATPase from bovine heart mitochondria (Bovine F1-ATPase crystallised in the absence of azide)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2CK3 | PDB ENTRY 2CK3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8.2 | 50 MM TRIS-HCL PH 8.2, 200 MM NACL, 20 MM MGSO4, 250 UM AMP-PNP, 5 UM ADP, 0.004% (W/V) PHENYLMETHYLSULFONYL FLUORIDE AND 12% (W/V) POLYETHYLENE GLYCOL 6000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.61 | α = 90 |
b = 123.13 | β = 90 |
c = 261.76 | 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 CCD | MIRRORS | 2006-11-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 |
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 | 1.9 | 20 | 72.8 | 0.06 | 15.9 | 3.1 | 194499 | 23.5 |
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 | 1.9 | 1.96 | 18.8 | 0.26 | 1.7 | 1.5 |
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 2CK3 | 1.9 | 20 | 184625 | 9777 | 72.7 | 0.177 | 0.175 | 0.22 | RANDOM | 20.58 |
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] | |
0.27 | 1.06 | -1.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.956 |
r_dihedral_angle_4_deg | 16.191 |
r_dihedral_angle_3_deg | 14.577 |
r_scangle_it | 7.651 |
r_scbond_it | 5.468 |
r_dihedral_angle_1_deg | 5.306 |
r_mcangle_it | 3.427 |
r_mcbond_it | 2.523 |
r_angle_refined_deg | 1.119 |
r_nbtor_refined | 0.298 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 23911 |
Nucleic Acid Atoms | |
Solvent Atoms | 2322 |
Heterogen Atoms | 160 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |