2XOK
Refined structure of yeast F1c10 ATPase complex to 3 A resolution
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2HLD | PDB ENTRY 2HLD |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | MICROBATCH | 8 | 0.1 M TRIS/CL PH8.0, 12% PEG 6000, 150 MM NACL, 1 MM AMP-PNP, 40 MICROM ADP, 1 MM DTT, 0.02% NAN3. MIXED 1:1 WITH PROTEIN SOLUTION UNDER PARAFFIN OIL IN MICROBATCH PLATE. | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.84 | 67.75 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 135.352 | α = 90 |
| b = 173.711 | β = 91.77 |
| c = 137.889 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | ADSC CCD | 1999-12-01 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 | |
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 | 3.01 | 20 | 74.8 | 0.09 | 4.1 | 1.8 | 93955 | 2 | 80.8 | ||||||||||
| 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 | 3 | 3.16 | 41.5 | 0.18 | 3.9 | 1.3 | |||||||||||||
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2HLD | 3.01 | 20 | 91603 | 2352 | 74.83 | 0.21066 | 0.20954 | 0.25335 | RANDOM | 116.881 | ||||||
| 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] | |
| 4.54 | 6.94 | -6.25 | 2.14 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.576 |
| r_dihedral_angle_3_deg | 20.207 |
| r_dihedral_angle_4_deg | 17.071 |
| r_scangle_it | 6.072 |
| r_dihedral_angle_1_deg | 6.01 |
| r_scbond_it | 3.642 |
| r_mcangle_it | 2.265 |
| r_angle_refined_deg | 1.368 |
| r_mcbond_it | 1.197 |
| r_nbtor_refined | 0.31 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 29953 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 160 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| AMoRE | phasing |
