4NZK
Crystal structure of a DHHW family protein (EUBSIR_00411) from Eubacterium siraeum DSM 15702 at 1.49 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 0.20M Sodium Iodide, 20.0% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.83 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.125 | α = 90 |
b = 102.125 | β = 90 |
c = 123.311 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | KOHZU: Double Crystal Si(111) | 2013-10-17 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 0.918401,0.979346,0.979261 | ALS | 8.2.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.49 | 29.481 | 100 | 0.11 | 12.5 | 10.3 | 62386 | 62386 |
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 | 1.49 | 1.53 | 100 | 0.015 | 1.482 | 0.5 | 10.3 | 4543 |
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 | 1.49 | 29.481 | 62267 | 3144 | 99.85 | 0.1264 | 0.1247 | 0.1577 | RANDOM | 19.684 |
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] | |
0.28 | 0.28 | 0.28 | -0.91 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.809 |
r_sphericity_free | 27.121 |
r_dihedral_angle_4_deg | 12.663 |
r_dihedral_angle_3_deg | 11.4 |
r_sphericity_bonded | 9.651 |
r_dihedral_angle_1_deg | 5.4 |
r_rigid_bond_restr | 3.424 |
r_mcangle_it | 2.6 |
r_mcbond_it | 2.208 |
r_mcbond_other | 2.202 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2389 |
Nucleic Acid Atoms | |
Solvent Atoms | 367 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
MolProbity | model building |
PDB_EXTRACT | data extraction |
SHELX | phasing |
SHARP | phasing |
SCALA | data scaling |
REFMAC | refinement |
MOSFLM | data reduction |
SHELXD | phasing |