1VMH
Crystal structure of an uncharacterized conserved protein yjbq/upf0047 family, ortholog yugu b.subtilis (ca_c0907) from clostridium acetobutylicum at 1.31 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP, NANODROP | 9 | 277 | 2.0% Dioxane, 10.0% PEG-20000, 0.1M Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.87 | 33.86 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.406 | α = 90 |
b = 79.406 | β = 90 |
c = 50.688 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
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 | ADSC QUANTUM 315 | Flat mirror | 2004-07-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-1 | SSRL | BL9-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.31 | 23.13 | 96.3 | 0.072 | 14.6 | 5.9 | 27579 | 22.87 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.31 | 1.38 | 85.5 | 0.654 | 1.7 | 1.9 | 3555 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1VMF | 1.31 | 23.13 | 26191 | 1388 | 96.25 | 0.15871 | 0.1574 | 0.18503 | RANDOM | 15.267 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.03 | -0.01 | -0.03 | 0.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.518 |
r_dihedral_angle_4_deg | 19.779 |
r_dihedral_angle_3_deg | 12.187 |
r_dihedral_angle_1_deg | 5.497 |
r_scangle_it | 4.714 |
r_scbond_it | 3.291 |
r_mcangle_it | 2.361 |
r_mcbond_it | 1.483 |
r_angle_refined_deg | 1.339 |
r_angle_other_deg | 0.785 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 995 |
Nucleic Acid Atoms | |
Solvent Atoms | 159 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
SCALA | data scaling |
MOLREP | phasing |
REFMAC | refinement |
XDS | data reduction |
CCP4 | data scaling |