1M32
Crystal Structure of 2-aminoethylphosphonate Transaminase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 277 | ammonium acetate, sodium citrate, mmPEG5K, PLP, phosphate, DTT, phosphonoacetaldehyde, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.66 | 53.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.6 | α = 90 |
b = 155.3 | β = 90.6 |
c = 168.6 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | MARRESEARCH | 1999-03-04 | M | MAD | ||||||
2 | 1 | x-ray | 100 | CCD | BRANDEIS - B4 | 1999-08-23 | M | MAD | ||||||
3 | 1 | x-ray | 100 | CCD | MARRESEARCH | 1999-03-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 0.9790, 0.9791, 0.95 | APS | 17-ID |
2 | SYNCHROTRON | NSLS BEAMLINE X12C | 0.9787, 0.9791, 0.95 | NSLS | X12C |
3 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.00 | APS | 17-ID |
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 | ||||||||
1,2,3 | 2.15 | 19.92 | 96.8 | 0.037 | 15.5 | 264452 | 264452 |
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) | |||||||||||
1,2,3 | 2.15 | 2.23 | 83 | 0.152 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | MAD | 2.2 | 20 | 2 | 128378 | 127266 | 12668 | 98.6 | 0.171 | 0.17 | 0.166 | 0.2 | random |
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 | |
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Key | Refinement Restraint Deviation |
c_angle_deg | 1.2 |
c_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16692 |
Nucleic Acid Atoms | |
Solvent Atoms | 3034 |
Heterogen Atoms | 118 |
Software
Software | |
---|---|
Software Name | Purpose |
DENZO | data reduction |
MADNESS | data collection |
TRUNCATE | data reduction |
cad | data reduction |
XPREP | data reduction |
AMoRE | phasing |
SHELXD | phasing |
MLPHARE | phasing |
DM | model building |
ARP/wARP | model building |
CNS | refinement |
MADNESS | data reduction |
CCP4 | data scaling |
CAD | data scaling |
DM | phasing |