4WE3
STRUCTURE OF THE BINARY COMPLEX OF A ZINGIBER OFFICINALE DOUBLE BOND REDUCTASE IN COMPLEX WITH NADP MONOCLINIC CRYSTAL FORM
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4NH4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293 | PEG 1500 24%, PCB 100 mM |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.57 | 52.06 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 131.704 | α = 90 |
b = 133.447 | β = 101.39 |
c = 90.942 | 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 | PIXEL | DECTRIS PILATUS 6M | mirrors | 2014-02-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.968630 | ESRF | ID23-1 |
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 | 2.49 | 46.4 | 99.3 | 0.089 | 0.101 | 11.04 | 4.51 | 53557 | 53557 | -3 | 59.919 |
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 | 2.49 | 2.58 | 99.1 | 0.998 | 1.125 | 1.74 | 4.61 |
Refinement
Statistics | |||||||||||||||||||
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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 | 4NH4 | 2.6 | 46.4 | 44714 | 2374 | 99.4 | 0.2245 | 0.2223 | 0.265 | RANDOM | 49.76 |
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] | |
-1.56 | -4.84 | -0.28 | 3.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.551 |
r_dihedral_angle_4_deg | 21.083 |
r_dihedral_angle_3_deg | 15.616 |
r_dihedral_angle_1_deg | 5.861 |
r_mcangle_it | 5.365 |
r_angle_other_deg | 3.775 |
r_mcbond_it | 3.53 |
r_mcbond_other | 3.528 |
r_angle_refined_deg | 1.501 |
r_chiral_restr | 0.082 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10141 |
Nucleic Acid Atoms | |
Solvent Atoms | 146 |
Heterogen Atoms | 192 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XSCALE | data scaling |
PHASER | phasing |
XSCALE | data reduction |