6R2U
Zinc-alpha2-Glycoprotein with a Fluorescent Dansyl C 11 Fatty Acid
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1T7V | 1t7v, pdbredo |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.4 | 294 | 1.3 M (NH4)2SO4, 100 mM Hepes |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.7 | 66.73 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 167.015 | ¦Á = 90 |
b = 167.015 | ¦Â = 90 |
c = 204.948 | ¦Ã = 90 |
Symmetry | |
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Space Group | I 4 |
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 PILATUS 6M-F | 2016-01-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 0.97949 | Diamond | I02 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.49 | 77.4 | 100 | 0.212 | 0.054 | 0.995 | 10 | 15.3 | 98002 | 51.29 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.49 | 2.53 | 99.2 | 3.388 | 0.856 | 0.298 | 1 | 15.6 |
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 | FREE R-VALUE | 1t7v, pdbredo | 2.49 | 77.4 | 95132 | 2698 | 99.98 | 0.17126 | 0.17019 | 0.21202 | RANDOM | 62.751 |
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] | |
-0.3 | -0.3 | 0.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.546 |
r_dihedral_angle_4_deg | 19.375 |
r_dihedral_angle_3_deg | 14.505 |
r_long_range_B_refined | 9.224 |
r_long_range_B_other | 9.224 |
r_scangle_other | 6.725 |
r_mcangle_it | 6.597 |
r_mcangle_other | 6.597 |
r_dihedral_angle_1_deg | 6.085 |
r_scbond_it | 4.631 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13369 |
Nucleic Acid Atoms | |
Solvent Atoms | 110 |
Heterogen Atoms | 313 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
Aimless | data scaling |
PHASER | phasing |