3TPY
Crystal structure of M-PMV dUTPase with a mixed population of substrate (dUPNPP) and post-inversion product (dUMP) in the active sites
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2D4L | PDB entry 2D4L |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | PEG 8000, AMMONIUM CHLORIDE, TRIS, PH 8.5, vapor diffusion, hanging drop, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.01 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.559 | α = 90 |
b = 60.559 | β = 90 |
c = 63.635 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | MAR CCD 165 mm | mirrors | 2003-02-09 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2003-03-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | 0.8028 | EMBL/DESY, HAMBURG | X13 |
2 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 1.0720 | ESRF | ID14-4 |
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 | ||||||||
1,2 | 1.75 | 20 | 99.8 | 0.032 | 44.8 | 11.4 | 13399 | 13399 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1,2 | 1.75 | 1.77 | 100 | 0.402 | 4.4 | 11.3 | 438 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | SIRAS | THROUGHOUT | PDB entry 2D4L | 1.75 | 20 | 13305 | 12600 | 705 | 99.03 | 0.1536 | 0.1517 | 0.1864 | RANDOM | 27.004 |
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] | |
0.79 | 0.4 | 0.79 | -1.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.517 |
r_dihedral_angle_4_deg | 28.651 |
r_dihedral_angle_3_deg | 15.274 |
r_scangle_it | 9.959 |
r_scbond_it | 6.941 |
r_dihedral_angle_1_deg | 5.745 |
r_mcangle_it | 3.509 |
r_mcbond_it | 2.722 |
r_angle_refined_deg | 1.957 |
r_nbtor_refined | 0.325 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 831 |
Nucleic Acid Atoms | |
Solvent Atoms | 131 |
Heterogen Atoms | 57 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
SOLVE | phasing |