4LOC
Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with oxamate and biotin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4JX4 | PDB ENTRY 4JX4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH CRYSTALLIZATION UNDER OIL | 6 | 298 | 14% (w/v) PEG 8000, 110 mM MOPS (pH 6.0), 165 mM Tetramethylammonium chloride, 2% (v/v) glycerol, BATCH CRYSTALLIZATION UNDER OIL, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.88 | 57.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.87 | α = 90 |
b = 157.123 | β = 90 |
c = 244.714 | 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 | 100 | CCD | MARMOSAIC 225 mm CCD | 2011-07-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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 | 2.26 | 50 | 98.3 | 0.084 | 20.6 | 7.1 | 148360 | 145868 | -3 | 34.4 |
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 | 2.26 | 2.3 | 94.7 | 0.444 | 3.4 | 6.8 |
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 | PDB ENTRY 4JX4 | 2.26 | 43.75 | 140726 | 7444 | 97.97 | 0.17837 | 0.17635 | 0.21628 | RANDOM | 50.934 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
4.52 | -1.78 | -2.74 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.428 |
r_dihedral_angle_4_deg | 19.813 |
r_dihedral_angle_3_deg | 15.782 |
r_dihedral_angle_1_deg | 6.359 |
r_long_range_B_refined | 5.794 |
r_long_range_B_other | 5.794 |
r_scangle_other | 2.931 |
r_mcangle_it | 2.462 |
r_mcangle_other | 2.462 |
r_scbond_it | 2.241 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 17888 |
Nucleic Acid Atoms | |
Solvent Atoms | 535 |
Heterogen Atoms | 111 |
Software
Software | |
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Software Name | Purpose |
MD2 | data collection |
PHASER | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |