1W6G
AGAO holoenzyme at 1.55 angstroms
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1AV4 | PDB ENTRY 1AV4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | THE CRYSTAL WAS GROWN BY HANGING DROP DIFFUSION AT 293K. THE RESERVOIR WAS 1.2M (NH4)2SO4, 12% DIOXANE, 0.1M MES PH6.5. THE DROP CONTAINED 1.5MICROLITER OF 11.7 MG/ML PROTEIN, 0.05M HEPES PH7.0, PLUS 1.5 MICROLITER OF RESERVOIR SOLUTION. A CRYSTAL WAS CRYOPROTECTED BY GRADUAL INCREMENTAL SOAKING IN RESERVOIR SOLUTION MIXED WITH GLYCEROL. THE CONCENTRATION OF GLYCEROL WAS INCREASED FROM 0 TO 30% IN 2-3% INCREMENTS DURING 2 HOURS. THE CRYSTAL WAS THEN FROZEN IN THE CRYOSTREAM., pH 7.00 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.03 | 59.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 157.836 | α = 90 |
b = 63.243 | β = 112.03 |
c = 91.982 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | IMAGE PLATE | MAR scanner 345 mm plate | 58 CM LONG, PT-COATED, FUSED SILICA, VERTICAL FOCUS MIRROR | 2002-03-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL7-1 | SSRL | BL7-1 |
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 | 1.55 | 25.85 | 96 | 0.04 | 10.83 | 1.92 | 117993 | -3 | 19.66 |
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 | 1.55 | 1.61 | 86.9 | 0.53 | 1.74 | 1.83 |
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 | THROUGHOUT | PDB ENTRY 1AV4 | 1.55 | 25.82 | 112062 | 5927 | 96.1 | 0.171 | 0.17 | 0.188 | RANDOM | 13.98 |
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] | |
-1.03 | -0.07 | 2.47 | -1.49 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 6.313 |
r_scangle_it | 5.771 |
r_scbond_it | 3.861 |
r_mcangle_it | 2.692 |
r_mcbond_it | 1.792 |
r_angle_refined_deg | 1.379 |
r_angle_other_deg | 0.797 |
r_symmetry_vdw_other | 0.315 |
r_nbd_other | 0.252 |
r_nbd_refined | 0.197 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4868 |
Nucleic Acid Atoms | |
Solvent Atoms | 506 |
Heterogen Atoms | 43 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |