3FXA
Crystal structure of a putative sugar-phosphate isomerase (lmof2365_0531) from listeria monocytogenes str. 4b f2365 at 1.60 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.9 | 277 | NANODROP, 0.2M Mg formate, 20.0% PEG 3350, No Buffer pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
2 | VAPOR DIFFUSION, SITTING DROP | 6.3 | 277 | NANODROP, 0.2M NH4Cl, 20.0% PEG 3350, No Buffer pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 57.944 | α = 90 |
b = 57.944 | β = 90 |
c = 197.964 | γ = 120 |
Symmetry | |
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Space Group | P 31 |
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 focusing mirrors in K-B geometry | 2008-10-11 | M | MAD | |||||
2 | 2 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | Adjustable focusing mirrors in K-B geometry | 2008-10-12 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.94645 | APS | 23-ID-B |
2 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.97966, 0.94645 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.6 | 28.976 | 99.6 | 0.085 | 0.085 | 5.726 | 4.7 | 97660 | 20.164 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1,2 | 1.6 | 1.64 | 97.2 | 0.652 | 0.652 | 1.8 | 3.3 | 7053 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD + MOLECULAR REPLACEMENT | THROUGHOUT | 1.6 | 28.976 | 97613 | 4850 | 99.5 | 0.135 | 0.133 | 0.157 | RANDOM + TWIN LAW | 18.562 |
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] | |
4.62 | 4.62 | -9.24 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.651 |
r_dihedral_angle_4_deg | 15.858 |
r_dihedral_angle_3_deg | 10.881 |
r_scangle_it | 4.574 |
r_dihedral_angle_1_deg | 3.473 |
r_scbond_it | 3.229 |
r_mcangle_it | 1.822 |
r_angle_refined_deg | 1.605 |
r_angle_other_deg | 1.339 |
r_mcbond_it | 1.154 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5695 |
Nucleic Acid Atoms | |
Solvent Atoms | 443 |
Heterogen Atoms | 8 |
Software
Software | |
---|---|
Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
SHELX | phasing |
SHARP | phasing |
PHASER | phasing |
REFMAC | refinement |
MolProbity | model building |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
SHELXD | phasing |
autoSHARP | phasing |