1VQU
Crystal structure of Anthranilate phosphoribosyltransferase 2 (17130499) from Nostoc sp. at 1.85 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1KGZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 293 | 20.025% PEG 3350, 0.2M Acetate_Na, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.47 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.556 | α = 90 |
b = 47.233 | β = 92.72 |
c = 99.376 | 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 | ADSC | 2003-10-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | ALS | 8.2.2 |
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 | 1.85 | 99.05 | 98.4 | 0.063 | 12.9 | 3.3 | 52559 | 41.56 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.85 | 1.9 | 99.7 | 0.749 | 1.3 | 2.8 | 3920 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1kgz | 1.85 | 99.05 | 49894 | 2636 | 97.95 | 0.18131 | 0.17921 | 0.2206 | RANDOM | 38.689 |
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] | |
1.25 | -0.58 | 1.45 | -2.75 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.868 |
r_dihedral_angle_4_deg | 18.49 |
r_dihedral_angle_3_deg | 15.845 |
r_scangle_it | 8 |
r_dihedral_angle_1_deg | 6.195 |
r_scbond_it | 5.61 |
r_mcangle_it | 3.556 |
r_mcbond_it | 2.422 |
r_angle_refined_deg | 1.569 |
r_angle_other_deg | 0.854 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4806 |
Nucleic Acid Atoms | |
Solvent Atoms | 229 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |
REFMAC | refinement |
CCP4 | data scaling |