4QSH
Crystal Structure of L. monocytogenes Pyruvate Carboxylase in complex with Cyclic-di-AMP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 298 | 19% PEG 3350, 0.2M Ammonium Citrate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.13 | 60.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96.778 | α = 90 |
b = 153.296 | β = 101.58 |
c = 221.24 | 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 QUANTUM 315 | MIRRORS | 2013-09-24 | 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 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 | 2.5 | 50 | 97.1 | 0.072 | 15.9 | 3.9 | 209169 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.5 | 2.59 | 87.3 | 0.38 | 3.3 | 3.4 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 3BG5 | 2.51 | 49.8 | 198499 | 10520 | 96.62 | 0.1965 | 0.19454 | 0.23336 | RANDOM | 55.768 |
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] | |
2.93 | -3.51 | -4.1 | 1.75 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.895 |
r_dihedral_angle_4_deg | 20.903 |
r_dihedral_angle_3_deg | 17.523 |
r_dihedral_angle_1_deg | 6.194 |
r_angle_refined_deg | 1.674 |
r_angle_other_deg | 1.083 |
r_chiral_restr | 0.093 |
r_bond_refined_d | 0.015 |
r_gen_planes_refined | 0.009 |
r_bond_other_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 33830 |
Nucleic Acid Atoms | |
Solvent Atoms | 506 |
Heterogen Atoms | 188 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |