4ZCU
Structure of calcium-bound regulatory domain of the human ATP-Mg/Pi carrier in the P2 form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4N5X |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 29% (w/v) PEG 8000, 0.2 M ammonium sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.86 | 56.98 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.08 | α = 90 |
b = 47.02 | β = 108.5 |
c = 93.24 | γ = 90 |
Symmetry | |
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Space Group | P 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 | 85 | CCD | MARMOSAIC 225 mm CCD | 2013-04-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.873 | ESRF | ID23-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | 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 | 39.393 | 99.8 | 0.119 | 0.079 | 0.993 | 7.3 | 3.2 | 36885 | 27.53 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.1 | 2.16 | 100 | 0.958 | 0.633 | 0.526 | 1.4 | 3.2 | 3050 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation 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 | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4N5X | 2.1 | 39.393 | 1.34 | 36863 | 1867 | 99.64 | 0.2383 | 0.2364 | 0.2745 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.424 |
f_angle_d | 0.829 |
f_chiral_restr | 0.031 |
f_bond_d | 0.01 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3747 |
Nucleic Acid Atoms | |
Solvent Atoms | 168 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
iMOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |