4AV3
Crystal structure of Thermotoga Maritima sodium pumping membrane integral pyrophosphatase with metal ions in active site
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 19-22% PEG 350, 0.1 M MES-NAOH PH 6.5, 0.2 M CA2CL, 2 MM DTT |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.96 | 58.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.52 | α = 90 |
b = 107.779 | β = 108.5 |
c = 102.521 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 100 | CCD | MARMOSAIC 225 mm CCD | RH-COATED SI MIRROR AND RH- COATED TOROIDAL SI MIRROR | 2012-02-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I911-3 | MAX II | I911-3 |
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 | 50 | 97.8 | 0.05 | 22.7 | 7.43 | 49279 | 2 |
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 | 2.6 | 2.76 | 95.1 | 0.84 | 2.14 | 6.9 |
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 | OUR BACKBONE HELICAL LOW RESOLUTION MODEL | 2.6 | 50 | 49279 | 2622 | 97.76 | 0.20658 | 0.20458 | 0.24478 | RANDOM | 71.691 |
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] | |
-6.51 | 1.57 | -0.08 | 7.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.917 |
r_dihedral_angle_3_deg | 19.878 |
r_dihedral_angle_4_deg | 16.994 |
r_dihedral_angle_1_deg | 6.356 |
r_angle_refined_deg | 1.703 |
r_angle_other_deg | 1.281 |
r_chiral_restr | 0.096 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 9965 |
Nucleic Acid Atoms | |
Solvent Atoms | 19 |
Heterogen Atoms | 4 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | model building |
XDS | data reduction |
XDS | data scaling |
SHELXCD | phasing |
SHELXD | phasing |
SHARP | phasing |
REFMAC | phasing |
PHENIX | phasing |