3K6C
Crystal structure of protein ne0167 from nitrosomonas europaea
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 298 | K/NA TARTRATE, PEG3350, PH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 45.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.417 | α = 90 |
b = 134.551 | β = 96.24 |
c = 78.458 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | CUSTOM-MADE | 2005-04-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.97924 | APS | 19-BM |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.2 | 50 | 99.9 | 0.099 | 26.3 | 7.1 | 50572 | 50559 | -3 | 35.3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.2 | 2.28 | 99 | 0.735 | 2.82 | 6.1 | 4980 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.2 | 50 | 50511 | 50511 | 2569 | 99.85 | 0.22291 | 0.22291 | 0.22075 | 0.26139 | RANDOM | 6.443 |
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] | |
-2.9 | -0.15 | 1.47 | 1.4 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.476 |
r_dihedral_angle_4_deg | 21.076 |
r_dihedral_angle_3_deg | 16.157 |
r_dihedral_angle_1_deg | 5.874 |
r_scangle_it | 2.924 |
r_scbond_it | 1.941 |
r_angle_refined_deg | 1.622 |
r_mcangle_it | 1.228 |
r_mcbond_it | 0.668 |
r_chiral_restr | 0.112 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7567 |
Nucleic Acid Atoms | |
Solvent Atoms | 344 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | phasing |
SHELXD | phasing |
SHELXE | model building |
MLPHARE | phasing |
DM | model building |
RESOLVE | model building |
Coot | model building |
ARP/wARP | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
DM | phasing |
RESOLVE | phasing |