3G68
CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOSUGAR ISOMERASE (CD3275) FROM CLOSTRIDIUM DIFFICILE 630 AT 1.80 A RESOLUTION
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 277 | NANODROP, 0.20M (NH4)2H Citrate, 20.0% PEG 3350, No Buffer pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 42.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 130.525 | α = 90 |
b = 55.914 | β = 114.22 |
c = 103.031 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | 100 | CCD | MARMOSAIC 325 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 | 0.97967, 0.94645 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.8 | 28.989 | 88.4 | 0.105 | 0.105 | 4.412 | 3.2 | 55259 | 13.458 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.8 | 1.85 | 43.3 | 0.247 | 0.247 | 3 | 1.6 | 1940 |
Refinement
Statistics | |||||||||||||||||||
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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 | THROUGHOUT | 1.8 | 28.989 | 55259 | 2802 | 88.06 | 0.161 | 0.159 | 0.194 | RANDOM | 17.311 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
-0.44 | -1.01 | -1.14 | 0.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.162 |
r_dihedral_angle_4_deg | 13.32 |
r_dihedral_angle_3_deg | 10.557 |
r_scangle_it | 4.989 |
r_dihedral_angle_1_deg | 3.845 |
r_scbond_it | 3.735 |
r_mcangle_it | 2.086 |
r_angle_refined_deg | 1.567 |
r_mcbond_it | 1.335 |
r_angle_other_deg | 1.157 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5427 |
Nucleic Acid Atoms | |
Solvent Atoms | 618 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
SHELX | phasing |
MolProbity | model building |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
MOSFLM | data reduction |
SHELXD | phasing |
autoSHARP | phasing |