4NG5
V203A horse liver alcohol dehydrogenase E 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 | PDB ENTRY 4DWV |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | MICRODIALYSIS | 7 | 278 | 50 mM ammonium N-[tris(hydrozymethyl)methyl]-2-aminoethanesulfonate and 0.5 mM EDTA, pH 6.7 (at 25 deg C), 10 mg/ml protein, 1 mM NAD+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 13-25 % 2-methyl-2,4-pentanediol, MICRODIALYSIS, temperature 278K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.42 | 49.16 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 44.52 | ¦Á = 91.8 |
b = 51.56 | ¦Â = 103.05 |
c = 92.55 | ¦Ã = 110.3 |
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 | MARMOSAIC 300 mm CCD | ADJUSTABLE FOCUS K-B PAIR SI PLUS PT, RH COATINGS DOUBLE CRYSTAL CRYOCOOLED SI(111) | 2007-06-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1.0332 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.1 | 20 | 86.2 | 0.068 | 15.5 | 5.25 | 261399 | 10.5 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.1 | 1.14 | 54.2 | 0.249 | 3.8 | 3.44 | 16455 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4DWV | 1.1 | 17.91 | 261399 | 258723 | 2681 | 86.19 | 0.11985 | 0.11985 | 0.11968 | 0.13655 | RANDOM | 17.529 |
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] | |
0.3 | -0.63 | 0.28 | 0.42 | 0.04 | -0.59 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.129 |
r_sphericity_free | 36.622 |
r_dihedral_angle_4_deg | 11.957 |
r_dihedral_angle_3_deg | 11.093 |
r_sphericity_bonded | 9.164 |
r_dihedral_angle_1_deg | 6.29 |
r_long_range_B_refined | 3.713 |
r_rigid_bond_restr | 3.337 |
r_long_range_B_other | 2.796 |
r_scangle_other | 2.343 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5566 |
Nucleic Acid Atoms | |
Solvent Atoms | 1052 |
Heterogen Atoms | 150 |
Software
Software | |
---|---|
Software Name | Purpose |
Blu-Ice | data collection |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |