3TZU
Crystal structure of a glycine cleavage system H protein (GCVH) from Mycobacterium marinum
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3IFT | PDB ENTRY 3IFT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 290 | Internal tracking number 219005, JCSG screen D04: 0.1 M acetate, pH 4.5, 200 mM lithium sulfate, 30% w/v PEG8000, MymaA.01046.b.A1 PS00874 16.35 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.29 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.31 | α = 90 |
b = 50.31 | β = 90 |
c = 165.32 | γ = 120 |
Symmetry | |
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Space Group | P 31 |
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 315r | 2011-09-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.97740 | ALS | 5.0.1 |
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 | 2.3 | 19.272 | 99.7 | 0.072 | 16.64 | 5.151 | 20756 | 20740 | -3 | -3 | 38.42 |
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 | 2.3 | 2.36 | 99.8 | 0.482 | 2.8 | 4.265 | 6624 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Number Reflections (All) | 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 | MR | THROUGHOUT | PDB ENTRY 3IFT | 2.3 | 19.272 | 2 | 20756 | 20740 | 1063 | 99.7 | 0.187 | 0.187 | 0.184 | 0.252 | RANDOM | 31.38 |
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] | |
-0.04 | -0.02 | -0.04 | 0.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.053 |
r_dihedral_angle_3_deg | 13.327 |
r_dihedral_angle_4_deg | 10.562 |
r_dihedral_angle_1_deg | 6.617 |
r_angle_refined_deg | 1.455 |
r_angle_other_deg | 0.91 |
r_chiral_restr | 0.079 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3590 |
Nucleic Acid Atoms | |
Solvent Atoms | 166 |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |