2PGV
GTB C209A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1LZ7 | GTB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 277 | 6.8 mgml-1 GTB, 70 mM N-(2-acetamido)-2-iminodiacetic acid (ADA), pH 7.5, 50 mM CH3COONa, pH 4.6, 40 mM NaCl, 5 8 mM MnCl2, 2.5% (v/v) 2-methyl-2,4-pentanediol (MPD), 5% (v/v) glycerol, 2% (w/v) PEG 4000 and 0.3 0.5 mM 3-chloro-Hg-2-methoxy-propylurea suspended over a 1 ml reservoir solution (50 mM ADA, pH 7.5, 10 mM MnCl2, 100 mM ammonium sulfate, 5% (v/v) MPD, 10% (v/v) glycerol and 8 10% (w/v) PEG 4000), VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.26 | 45.57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.5 | α = 90 |
b = 149.26 | β = 90 |
c = 78.43 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | 113 | IMAGE PLATE | RIGAKU RAXIS IV | Osmic | 2006-05-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU |
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 | 1.79 | 19.76 | 93.5 | 0.049 | 13.3 | 3.99 | 27550 |
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 | 1.79 | 1.85 | 89.1 | 0.311 | 3.6 | 3.89 |
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 | GTB | 1.79 | 19.76 | 26134 | 1409 | 93.45 | 0.18731 | 0.18593 | 0.21254 | RANDOM |
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] | |
-0.86 | -0.38 | 1.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.047 |
r_dihedral_angle_4_deg | 18.026 |
r_dihedral_angle_3_deg | 14.1 |
r_dihedral_angle_1_deg | 6.204 |
r_scangle_it | 3.532 |
r_scbond_it | 2.258 |
r_mcangle_it | 1.457 |
r_angle_refined_deg | 1.437 |
r_mcbond_it | 0.942 |
r_nbtor_refined | 0.308 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2213 |
Nucleic Acid Atoms | |
Solvent Atoms | 191 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |
d*TREK | data reduction |
MOLREP | phasing |