4X1J
X-ray crystal structure of the dimeric BMP antagonist NBL1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.1 MES/imidazole (pH 6.5) and 0.02M of several amino acids (sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.55 | 56.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.665 | α = 90 |
b = 59.665 | β = 90 |
c = 145.018 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | 80 | CCD | MARMOSAIC 300 mm CCD | 2013-12-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 0.979 | APS | 21-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.5 | 55.18 | 99.68 | 23.5 | 12.3 | 9690 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | THROUGHOUT | 2.5 | 55.18 | 8674 | 964 | 99.68 | 0.22175 | 0.21576 | 0.27315 | RANDOM | 89.054 |
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] | |
0.25 | 0.25 | -0.49 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_bonded | 43.6 |
r_dihedral_angle_2_deg | 35.874 |
r_long_range_B_refined | 16.68 |
r_long_range_B_other | 16.676 |
r_dihedral_angle_3_deg | 15.946 |
r_scangle_other | 15.747 |
r_scbond_it | 12.385 |
r_scbond_other | 12.152 |
r_dihedral_angle_4_deg | 10.462 |
r_mcangle_it | 9.017 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1330 |
Nucleic Acid Atoms | |
Solvent Atoms | 5 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |