4Q52
2.60 Angstrom resolution crystal structure of a conserved uncharacterized protein from Chitinophaga pinensis DSM 2588
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 295 | protein: 7.8 mg/mL in 10 mM Tris/HCl, 500 mM NaCl, 5 mM BME crystallization: the PACT Suite (C11: 0.2 M CaCl2, 0.1 M HEPES pH 7.0, 20 % (w/v) PEG 6000) cryo: 25 % glucose, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.35 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.712 | α = 90 |
b = 85.549 | β = 104.19 |
c = 88.195 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | MARMOSAIC 225 mm CCD | Be lenses | 2014-02-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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 | 2.6 | 30 | 99.9 | 0.152 | 0.152 | 12.2 | 4.8 | 22847 | 22847 | -3 | 44.1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.6 | 2.64 | 100 | 0.641 | 2.5 | 4.8 | 1110 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | SAD | THROUGHOUT | 2.6 | 29.19 | 21649 | 21649 | 1167 | 99.53 | 0.17114 | 0.16869 | 0.21529 | RANDOM | 34.912 |
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] | |
0.43 | 0.64 | -2.67 | 1.84 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_4_deg | 33.075 |
r_dihedral_angle_2_deg | 30.116 |
r_dihedral_angle_3_deg | 12.377 |
r_dihedral_angle_1_deg | 4.539 |
r_angle_refined_deg | 1.62 |
r_angle_other_deg | 1.057 |
r_chiral_restr | 0.09 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.009 |
r_bond_other_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5306 |
Nucleic Acid Atoms | |
Solvent Atoms | 229 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
HKL-3000 | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |