4MZW
CRYSTAL STRUCTURE OF NU-CLASS GLUTATHIONE TRANSFERASE YGHU FROM Streptococcus sanguinis SK36, COMPLEX WITH GLUTATHIONE DISULFIDE, TARGET EFI-507286
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3C8E | PDB ENTRY 3C8E |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 1.1M Malonic Acid, 0.15M Ammonium Citrate Tribasic, 0.072M Succinic Acid, 0.18M DL-Malic Acid, 0.24M Sodium Acetate, 0.3M Sodium Formate, 0.096M Ammonium Tartrate Dibasic, pH 7.0, 5MM GSH, PROTEIN IN 10MM HEPES, PH 7.5, 150MM SODIUM CHLORIDE, 5% GLYCEROL, CRYOPROTECTANT: NONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.51 | 51.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 88.075 | α = 90 |
b = 88.075 | β = 90 |
c = 163.373 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | ADSC QUANTUM 315 | MIRRORS | 2013-09-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.95 | 50 | 99.3 | 0.075 | 9.8 | 13.2 | 47570 | -5 |
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 | 1.95 | 1.98 | 100 | 0.76 | 3.5 | 13.5 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3C8E | 1.95 | 50 | 45722 | 1476 | 99.02 | 0.15288 | 0.15154 | 0.17 | 0.19383 | 0.2 | RANDOM | 40.471 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
0.9 | 0.9 | -1.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.859 |
r_dihedral_angle_4_deg | 17.436 |
r_scangle_other | 13.846 |
r_dihedral_angle_3_deg | 13.456 |
r_long_range_B_refined | 13.05 |
r_long_range_B_other | 13.034 |
r_scbond_it | 12.613 |
r_scbond_other | 12.611 |
r_mcangle_other | 10.339 |
r_mcangle_it | 10.331 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4169 |
Nucleic Acid Atoms | |
Solvent Atoms | 472 |
Heterogen Atoms | 84 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |