3P7I
Crystal structure of Escherichia coli PhnD in complex with 2-aminoethyl phosphonate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 298.15 | 0.2M ammonium sulfate, sodium acetate trihydrate, pH 4.6, 25% w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.39 | 48.63 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 76.094 | ¦Á = 90 |
b = 82.44 | ¦Â = 90 |
c = 54.667 | ¦Ã = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 2 |
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 | MAR CCD 165 mm | 2009-04-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.9793 | APS | 31-ID |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.71 | 45.6 | 99.6 | 35864 | 35721 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.71 | 45.6 | 35864 | 35721 | 1880 | 99.6 | 0.22697 | 0.22697 | 0.22568 | 0.25144 | RANDOM | 25.239 |
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] | |
-0.04 | 0.05 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 42.228 |
r_dihedral_angle_4_deg | 18.994 |
r_dihedral_angle_3_deg | 16.728 |
r_dihedral_angle_1_deg | 5.956 |
r_scangle_it | 5.051 |
r_scbond_it | 3.215 |
r_mcangle_it | 2.077 |
r_angle_refined_deg | 2.021 |
r_mcbond_it | 1.319 |
r_chiral_restr | 0.151 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2353 |
Nucleic Acid Atoms | |
Solvent Atoms | 143 |
Heterogen Atoms | 25 |
Software
Software | |
---|---|
Software Name | Purpose |
SPEC | data collection |
PHASER | phasing |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |