3N8G
Structure of the (SR)Ca2+-ATPase Ca2-E1-CaAMPPCP form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1T5S | PDB ENTRY 1T5S |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.8 | 292 | PEG 6000, ter-butanol, sodium acetate, potassium chloride, magnesium chloride, glycerol, MOPS, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 929Kk, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.03 | 69.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 162 | α = 90 |
b = 76 | β = 108 |
c = 151 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | CCD | MARRESEARCH | 2004-01-13 | M | SINGLE WAVELENGTH | |||||||
2 | 1 | x-ray | CCD | ADSC QUANTUM 4 | 2004-02-04 | M | SINGLE WAVELENGTH | |||||||
3 | 1 | x-ray | CCD | ADSC QUANTUM 4 | 2004-02-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | BESSY | 14.1 | |
2 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 | |
3 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 |
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 | 2.6 | 40 | 99.8 | 0.092 | 7 | 53349 | 53349 | -3 | 77 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.6 | 2.66 | 100 | 0.75 | 0.75 | 2.8 | 6.6 | 3518 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | Re-refinement | PDB ENTRY 1T5S | 2.585 | 30.132 | 1.34 | 54059 | 1529 | 98.36 | 0.2035 | 0.2022 | 0.2455 | Random | 63.75 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
1.4474 | 2.3325 | -5.4049 | 3.9575 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.086 |
f_angle_d | 1.093 |
f_chiral_restr | 0.076 |
f_bond_d | 0.007 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7671 |
Nucleic Acid Atoms | |
Solvent Atoms | 92 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |