6CIB
The structure of YcaO from Methanopyrus kandleri bound with AMPPCP and Mg2+
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 282.1 | 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate (tribasic), 0.02 M sodium potassium tartrate, 0.02 M sodium oxamate, 0.05 M HEPES pH=7.5, 0.05 M MOPS pH=7.5, 20% glycerol, and 10% PEG 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.44 | 64.25 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 123.232 | ¦Á = 90 |
b = 105.627 | ¦Â = 103.64 |
c = 139.298 | ¦Ã = 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 | 80 | PIXEL | DECTRIS EIGER X 9M | 2017-08-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.07822 | APS | 21-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.04 | 80.7 | 90.8 | 9.8 | 4.1 | 200362 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.05 | 2.103 |
Refinement
Statistics | |||||||||||||||||||
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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 | THROUGHOUT | 2.05 | 25 | 187537 | 9774 | 90.77 | 0.19652 | 0.19459 | 0.23361 | RANDOM | 40.236 |
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] | |
-2.28 | 0.52 | 0.95 | 0.96 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.473 |
r_dihedral_angle_4_deg | 16.616 |
r_dihedral_angle_3_deg | 16.111 |
r_long_range_B_refined | 6.196 |
r_dihedral_angle_1_deg | 5.58 |
r_mcangle_it | 2.83 |
r_scbond_it | 2.383 |
r_mcbond_it | 1.7 |
r_angle_refined_deg | 1.352 |
r_chiral_restr | 0.087 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 17352 |
Nucleic Acid Atoms | |
Solvent Atoms | 1538 |
Heterogen Atoms | 204 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
SHARP | phasing |