8G4V
Horse liver alcohol dehydrogense His-51-Gln form complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 4DWV |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | MICRODIALYSIS | 7 | 278 | 10 mg/ml protein in 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfate buffer with 0.25 mM EDTA, 2 mM NAD+ and 15 mM 2,3,4,5,6-pentafluorobenzyl alcohol, crystals formed at ~13 % 2-methyl-2,4-pentanediol, raised to 25% MPD before crystal pliunged into liquid N2. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.28 | 46 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 44.17 | α = 92.02 |
b = 51.59 | β = 102.89 |
c = 92.77 | γ = 110.04 |
Symmetry | |
---|---|
Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210 | 2004-07-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.000 | APS | 17-ID |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.2 | 19.96 | 91.1 | 0.06 | 0.065 | 13.3 | 6.13 | 211946 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.2 | 1.24 | 74.4 | 0.181 | 0.212 | 3.5 |
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 | 4dwv | 1.2 | 19.96 | 207414 | 2091 | 89.98 | 0.13518 | 0.13493 | 0.1607 | RANDOM | 17.445 |
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] | |
0.19 | -0.33 | 0.06 | 0.53 | 0.11 | -0.61 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.392 |
r_dihedral_angle_4_deg | 13.729 |
r_dihedral_angle_3_deg | 12.183 |
r_dihedral_angle_1_deg | 6.595 |
r_rigid_bond_restr | 4.988 |
r_scangle_other | 3.215 |
r_scbond_it | 3.139 |
r_scbond_other | 3.139 |
r_long_range_B_refined | 2.968 |
r_long_range_B_other | 2.85 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5568 |
Nucleic Acid Atoms | |
Solvent Atoms | 673 |
Heterogen Atoms | 126 |
Software
Software | |
---|---|
Software Name | Purpose |
d*TREK | data scaling |
REFMAC | refinement |
d*TREK | data reduction |
O | model building |