1VK6
Crystal structure of NADH pyrophosphatase (1790429) from Escherichia coli k12 at 2.20 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 277 | 12% MPD, 0.08M HEPES, 0.02M HEPES_Na , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.13 | 69.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 127.319 | α = 90 |
b = 127.319 | β = 90 |
c = 108.405 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC | 2003-10-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | ALS | 8.3.1 |
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 | 2.2 | 63.66 | 100 | 0.068 | 13.9 | 7.4 | 26842 | 53.64 |
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 | 2.2 | 2.32 | 100 | 0.588 | 2.3 | 4.7 | 3836 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.2 | 63.66 | 25436 | 1371 | 99.87 | 0.18831 | 0.18668 | 0.21955 | RANDOM | 68.881 |
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] | |
1.85 | 0.92 | 1.85 | -2.77 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.71 |
r_dihedral_angle_4_deg | 15.135 |
r_dihedral_angle_3_deg | 14.851 |
r_scangle_it | 7.928 |
r_scbond_it | 6.251 |
r_dihedral_angle_1_deg | 5.824 |
r_mcangle_it | 3.466 |
r_mcbond_it | 2.452 |
r_angle_refined_deg | 1.509 |
r_symmetry_vdw_refined | 0.201 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2053 |
Nucleic Acid Atoms | |
Solvent Atoms | 96 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |
CNS | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |
CNS | phasing |