4BMN
apo structure of short-chain alcohol dehydrogenase from Ralstonia sp. DSM 6428
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4FGS | PDB ENTRY 4FGS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 0.1M BIS-TRIS PROPANE PH 7.0 CONTAINING 20% (W/V) PEG 3350 AND 0.02 M SODIUM-POTASSIUM PHOSPHATE. THE PROTEIN CONCENTRATION WAS 24 MG ML-1. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.9 | 35 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 136.48 | α = 90 |
b = 52.51 | β = 116.57 |
c = 151.47 | 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 | 120 | CCD | ADSC CCD | 2013-02-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | Diamond | I02 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.52 | 60.86 | 97.7 | 0.03 | 15.6 | 3.3 | 149646 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.52 | 1.57 | 96.8 | 0.25 | 4.9 | 3.5 |
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 | PDB ENTRY 4FGS | 1.5 | 60.86 | 141654 | 7501 | 96.94 | 0.15962 | 0.15812 | 0.18784 | RANDOM | 21.997 |
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] | |
-0.66 | 0.12 | 1.87 | -0.89 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.71 |
r_dihedral_angle_4_deg | 11.306 |
r_dihedral_angle_3_deg | 11.088 |
r_dihedral_angle_1_deg | 6.344 |
r_scbond_it | 3.091 |
r_mcangle_it | 2.88 |
r_mcbond_it | 2.124 |
r_mcbond_other | 2.123 |
r_angle_refined_deg | 2.122 |
r_angle_other_deg | 1.683 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6877 |
Nucleic Acid Atoms | |
Solvent Atoms | 847 |
Heterogen Atoms | 43 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |