4DWV
Horse alcohol dehydrogenase complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1HLD | pdb entry 1HLD |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICRODIALYSIS | 6.7 | 278 | 50 mm ammonium n-[tris(hydroxymethyl) methyl]-2-aminoethane sulfonate, ph 6.7 (at 25 c), 0.25 mm edta, 10 mg/ml protein, 1 mm nad+, 10 mm 2,3,4,5,6-pentafluorobenzyl alcohol, 12 to 25 % 2-methyl-2,4-pentanediol, MICRODIALYSIS, temperature 278k |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.29 | α = 91.72 |
b = 51.44 | β = 103.09 |
c = 92.49 | γ = 110.11 |
Symmetry | |
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Space Group | P 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 | CCD | MARMOSAIC 300 mm CCD | ADJUSTABLE FOCUS K-B PAIR SI PLUS PT, RH COATINGS | 2006-03-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.9537 | APS | 23-ID-D |
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 | 1.14 | 20 | 93.7 | 0.065 | 12.9 | 4.75 | 270489 | 253394 | 1 | 1 |
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 | 1.14 | 1.18 | 84.5 | 0.264 | 3.2 | 3.74 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 1HLD | 1.14 | 20 | 270489 | 250826 | 2572 | 93.65 | 0.12406 | 0.12387 | 0.14373 | RANDOM | 14.926 |
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] | |
0.11 | -0.5 | 0.21 | 0.26 | -0.06 | -0.63 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.256 |
r_sphericity_free | 31.716 |
r_dihedral_angle_4_deg | 13.883 |
r_dihedral_angle_3_deg | 11.32 |
r_sphericity_bonded | 9.439 |
r_dihedral_angle_1_deg | 6.24 |
r_scangle_it | 4.734 |
r_rigid_bond_restr | 3.422 |
r_scbond_it | 3.168 |
r_mcangle_it | 2.191 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5570 |
Nucleic Acid Atoms | |
Solvent Atoms | 1040 |
Heterogen Atoms | 150 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
AMoRE | phasing |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |