2O3L
Crystal structure of a duf1048 protein with a left-handed superhelix fold (bce_3448) from bacillus cereus atcc 10987 at 2.05 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP, NANODROP | 6 | 277 | 0.8M (NH4)2SO4, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.78 | 55.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.202 | α = 90 |
b = 61.202 | β = 90 |
c = 101.702 | 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 | 100 | CCD | MARMOSAIC 300 mm CCD | Adjustable focusing mirrors in K-B geometry | 2006-10-19 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.97921, 0.97942, 0.94645 | APS | 23-ID-D |
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 | 1.999 | 29.298 | 99.8 | 0.071 | 0.071 | 6.4 | 5.2 | 14352 | 31.23 |
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 | 2.05 | 2.1 | 99.3 | 0.635 | 0.635 | 1.1 | 5.1 | 1040 |
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 | THROUGHOUT | 2.05 | 29.298 | 14319 | 723 | 99.82 | 0.186 | 0.184 | 0.227 | RANDOM | 39.551 |
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] | |
0.87 | 0.43 | 0.87 | -1.3 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.524 |
r_dihedral_angle_3_deg | 14.636 |
r_dihedral_angle_4_deg | 9.518 |
r_scangle_it | 8.363 |
r_scbond_it | 6.955 |
r_dihedral_angle_1_deg | 5.699 |
r_mcangle_it | 3.489 |
r_mcbond_it | 2.487 |
r_angle_refined_deg | 1.501 |
r_angle_other_deg | 0.858 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1263 |
Nucleic Acid Atoms | |
Solvent Atoms | 106 |
Heterogen Atoms | 23 |
Software
Software | |
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Software Name | Purpose |
MolProbity | model building |
SHELX | phasing |
REFMAC | refinement |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
CCP4 | data scaling |
SHELXD | phasing |
autoSHARP | phasing |