4ZEY
Crystal structure of a nuclear receptor binding factor 2 MIT domain (NRBF2) from Homo sapiens at 1.50 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 25.0% Glycerol, 1.50M ammonium sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.83 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.48 | α = 90 |
b = 34.05 | β = 108.47 |
c = 52.34 | 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 | 100 | CCD | MARMOSAIC 325 mm CCD | Vertical focusing mirror; double crystal Si(111) monochromator | 2014-12-05 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL14-1 | 0.95369,0.97968,0.97943 | SSRL | BL14-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.5 | 27.366 | 92.4 | 0.092 | 0.128 | 7.56 | 1.685 | 12873 | -3 | 17.415 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.5 | 1.55 | 92.1 | 0.392 | 0.538 | 1.8 |
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 | MAD | THROUGHOUT | 1.5 | 27.366 | 12871 | 618 | 97.92 | 0.2107 | 0.2089 | 0.2482 | RANDOM | 25.7253 |
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] | |
1.4756 | 0.504 | -2.3193 | 0.8436 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_omega_torsion | 2.49 |
t_other_torsion | 2.49 |
t_angle_deg | 0.9 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 679 |
Nucleic Acid Atoms | |
Solvent Atoms | 102 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
PDB_EXTRACT | data extraction |
SOLVE | phasing |
XSCALE | data scaling |
BUSTER-TNT | refinement |
BUSTER | refinement |
XDS | data reduction |