6C76
Structure of Iron containing alcohol dehydrogenase from Thermococcus thioreducens in an orthorhombic crystal form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6C75 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 298 | 0.1 M sodium acetate, 10% PEG 10,000 at pH 4.6 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.34 | 47 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.92 | α = 90 |
b = 111.978 | β = 90 |
c = 142.081 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 298 | CCD | RIGAKU SATURN 944+ | OSMIC MIRRORS | 2013-04-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54187 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2.1 | 43.97 | 90 | 0.209 | 0.214 | 0.041 | 0.995 | 13 | 20.4 | 41831 | 36.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.1 | 2.16 | 35.6 | 0.974 | 1.192 | 0.67 | 0.222 | 0.7 | 2.4 |
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 | 6C75 | 2.1 | 33.04 | 39750 | 2018 | 89.82 | 0.15633 | 0.15387 | 0.20419 | RANDOM | 46.619 |
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] | |
-0.03 | 0.98 | -0.95 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.979 |
r_dihedral_angle_4_deg | 23.011 |
r_dihedral_angle_3_deg | 18.033 |
r_long_range_B_refined | 10.5 |
r_long_range_B_other | 10.478 |
r_scangle_it | 7.737 |
r_scangle_other | 7.737 |
r_dihedral_angle_1_deg | 7.442 |
r_mcangle_other | 4.997 |
r_mcangle_it | 4.995 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5852 |
Nucleic Acid Atoms | |
Solvent Atoms | 293 |
Heterogen Atoms | 63 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |