5OJG
Crystal structure of the dehydrogenase/reductase SDR family member 4 (DHRS4) from Caenorhabditis elegans
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3O4R |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | 10 % (w/v) PEG 8000 200 mM NaCl 100 mM K/Na-phospate pH 6.2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.62 | 53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 93.6 | α = 90 |
b = 93.6 | β = 90 |
c = 132.01 | γ = 90 |
Symmetry | |
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Space Group | P 42 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 | 100 | PIXEL | DECTRIS PILATUS3 6M | 2013-05-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 0.976261 | PETRA III, EMBL c/o DESY | P14 (MX2) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.9 | 76.35 | 99.9 | 0.489 | 0.995 | 8.3 | 23.3 | 46906 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.9 | 1.95 | 99.9 | 5.039 | 0.214 |
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 | 3O4R | 1.9 | 76.35 | 44560 | 2346 | 99.95 | 0.18133 | 0.17911 | 0.22344 | RANDOM | 35.408 |
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] | |
0.71 | 0.71 | -1.42 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.573 |
r_dihedral_angle_4_deg | 14.045 |
r_dihedral_angle_3_deg | 13.79 |
r_long_range_B_refined | 8.728 |
r_long_range_B_other | 8.586 |
r_dihedral_angle_1_deg | 6.838 |
r_scangle_other | 6.103 |
r_mcangle_it | 4.525 |
r_mcangle_other | 4.525 |
r_scbond_it | 4.075 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3880 |
Nucleic Acid Atoms | |
Solvent Atoms | 509 |
Heterogen Atoms | 108 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | phasing |