1VPH
CRYSTAL STRUCTURE OF a YbjQ-like protein of unknown function (SSO2532) FROM SULFOLOBUS SOLFATARICUS P2 AT 1.76 A RESOLUTION
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 7.5 | 277 | 10.0% iso-Propanol, 20.0% PEG-4000, 0.1M HEPES pH7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.13 | 41.76 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.86 | α = 90 |
b = 92.18 | β = 90 |
c = 114.13 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 2004-07-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | SSRL | BL9-2 |
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 | 1.764 | 28.68 | 90.9 | 0.062 | 15.6 | 3.9 | 75897 | 31.06 |
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 | 1.764 | 1.86 | 63.6 | 0.312 | 3 | 1.9 | 7634 |
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 | 1VMF | 1.764 | 16.22 | 72013 | 3791 | 90.69 | 0.19082 | 0.18914 | 0.22173 | RANDOM | 22.167 |
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] | |
0.58 | -2.01 | 1.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.54 |
r_dihedral_angle_3_deg | 14.27 |
r_dihedral_angle_4_deg | 11.353 |
r_scangle_it | 6.712 |
r_dihedral_angle_1_deg | 6.46 |
r_scbond_it | 4.767 |
r_mcangle_it | 2.714 |
r_angle_refined_deg | 1.607 |
r_mcbond_it | 1.599 |
r_angle_other_deg | 0.961 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6658 |
Nucleic Acid Atoms | |
Solvent Atoms | 286 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
SOLVE | phasing |
SCALA | data scaling |
MOLREP | phasing |
REFMAC | refinement |
CCP4 | data scaling |