4JX5
Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with pyruvate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2QF7 | CT+ALLOSTERIC DOMAIN (RESI 471-1067) OF PDB ENTRY 2QF7 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | BATCH CRYSTALLIZATION UNDER OIL | 6 | 298 | 11.3 (w/v) PEG 8000, 99 mM BisTris (pH 6.0), 346 mM Tetramethylammonium chloride , BATCH CRYSTALLIZATION UNDER OIL, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.93 | 58.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 85.13 | α = 90 |
b = 157.253 | β = 90 |
c = 245.32 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | MARMOSAIC 300 mm CCD | 2012-03-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.55 | 50 | 99.8 | 0.085 | 24 | 7.2 | 107850 | 107658 | -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 | 2.55 | 2.59 | 99.9 | 0.444 | 4.4 | 7.1 |
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 | CT+ALLOSTERIC DOMAIN (RESI 471-1067) OF PDB ENTRY 2QF7 | 2.55 | 46.88 | 102382 | 5384 | 99.46 | 0.18888 | 0.1866 | 0.2321 | RANDOM | 68.802 |
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] | |
7.93 | -2.87 | -5.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.213 |
r_dihedral_angle_4_deg | 21.263 |
r_dihedral_angle_3_deg | 16.298 |
r_dihedral_angle_1_deg | 6.117 |
r_mcangle_it | 2.693 |
r_scbond_it | 2.2 |
r_mcbond_it | 1.699 |
r_angle_refined_deg | 1.513 |
r_chiral_restr | 0.097 |
r_bond_refined_d | 0.012 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 17668 |
Nucleic Acid Atoms | |
Solvent Atoms | 207 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
MD2 | data collection |
PHASER | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |