2GCU
X-Ray Structure of Gene Product from Arabidopsis Thaliana At1g53580
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 297 | 24% MEPEG 5K, 0.10 M HEPES PH 8.5, 0.050 M MAGNESIUM SULFATE, vapor diffusion, hanging drop, temperature 297K | |
2 | VAPOR DIFFUSION, HANGING DROP | 297 | 25% MEPEG 5K, 0.10 M HEPES PH 8.5, 0.050 M MAGNESIUM SULFATE (PHASING CRYSTAL SOAKED 2 DAYS IN ABOVE WELL SOLUTION PLUS 0.002 M THIMEROSAL), vapor diffusion, hanging drop, temperature 297K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.607 | α = 90 |
b = 64.469 | β = 97.83 |
c = 127.877 | 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 300 mm CCD | HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR | 2005-06-13 | M | SINGLE WAVELENGTH | |||||
2 | 2 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | PAIR OF BIMORPH, RHODIUM COATED KIRKPATRICK-BAEZ MIRRORS | 2005-08-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.23984 | APS | 22-ID |
2 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.98244 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.48 | 50 | 94.6 | 0.075 | 12.429 | 5.9 | 170395 |
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 | 1.48 | 1.51 | 67.7 | 0.435 | 2.818 | 2.5 | 8076 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.477 | 46.127 | 170375 | 8539 | 94.818 | 0.178 | 0.17791 | 0.1765 | 0.2037 | RANDOM | 19.368 |
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] | |
-0.001 | 0.001 | 0.002 | -0.001 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.78 |
r_dihedral_angle_3_deg | 11.706 |
r_dihedral_angle_4_deg | 8.594 |
r_dihedral_angle_1_deg | 6.186 |
r_scangle_it | 4.22 |
r_scbond_it | 2.762 |
r_mcangle_it | 1.764 |
r_angle_refined_deg | 1.636 |
r_mcbond_it | 1.14 |
r_nbtor_refined | 0.307 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7422 |
Nucleic Acid Atoms | |
Solvent Atoms | 1037 |
Heterogen Atoms | 65 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SHARP | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PHENIX | phasing |
ARP/wARP | model building |