3QUT
Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron, asp13asn mutant, an open cap conformation
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3QU2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 0.15M MALIC ACID, PH 7, 20% PEG3350, 5MM MAGNESIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 45.475 | α = 90 |
b = 65.405 | β = 90 |
c = 76.168 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 90 | CCD | ADSC QUANTUM 315 | MIRRORS | 2010-01-23 | 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 | 1.5 | 50 | 100 | 0.067 | 7.4 | 8 | 37187 | -5 | 18.419 |
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 | 1.5 | 1.53 | 100 | 0.6 | 3 | 7.5 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MR | THROUGHOUT | 3QU2 | 1.5 | 49.63 | 35951 | 1152 | 99.96 | 0.14545 | 0.14457 | 0.17227 | RANDOM | 25.063 |
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] | |
0.32 | 0.42 | -0.74 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.779 |
r_dihedral_angle_4_deg | 22.207 |
r_dihedral_angle_3_deg | 14.948 |
r_scangle_it | 9.836 |
r_scbond_it | 7.27 |
r_dihedral_angle_1_deg | 5.717 |
r_mcangle_it | 5.525 |
r_mcbond_it | 3.908 |
r_rigid_bond_restr | 2.546 |
r_angle_refined_deg | 1.387 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1752 |
Nucleic Acid Atoms | |
Solvent Atoms | 243 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |