1C4K
ORNITHINE DECARBOXYLASE MUTANT (GLY121TYR)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ORD | 1ORD, MOLECULE A. |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 7 | 20 DEG, SITTING DROP, MICROBRIDGES, RESERVOIRS CONTAINING 30% PEG3350, 0.2 M AMMONIUM ACETATE, AND 0.1 M SODIUM HEPES PH 7.0. DROPS CONSISTED OF EQUAL VOLUMES RESERVOIR AND 20 MG/ML PROTEIN SOLUTION. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.96 | 58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 111.8 | α = 90 |
b = 111.8 | β = 90 |
c = 135.9 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 295 | IMAGE PLATE | RIGAKU RAXIS IV | MSC MIRRORS | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.7 | 50 | 94.3 | 0.069 | 17.5 | 2.8 | 26013 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.7 | 2.8 | 95.1 | 0.358 | 2.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | R-FREE | 1ORD, MOLECULE A. | 2.7 | 7 | 2 | 24164 | 2374 | 94.4 | 0.212 | 0.212 | 0.281 | RANDOM | 40.6 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
x_angle_deg | 1.8 |
x_improper_angle_d | 1.6 |
x_bond_d | 0.013 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na | |
x_angle_deg_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5826 |
Nucleic Acid Atoms | |
Solvent Atoms | 250 |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | model building |
X-PLOR | refinement |
X-PLOR | phasing |