2BSL
Crystal structure of L. lactis dihydroorotate dehydrogense A in complex with 3,4-dihydroxybenzoate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1OVD | PDB ENTRY 1OVD |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 17 MG/ML PROTEIN AND 2.6 MM 3, 4-DIOHB HANGING DROPS 2 MICROLITERS OF PROTEIN AND 2 MICROLITERS RESERVOIR: 30 % PEG 6000, 1 MM DTT, 0.2 M SODIUM ACETATE AND 0.1 M TRIS-HCL PH 8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.62 | 54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.588 | α = 90 |
b = 108.16 | β = 104.06 |
c = 66.222 | 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 | 120 | IMAGE PLATE | MARRESEEARCH | MIRRORS | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU300 |
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 | 2.3 | 25 | 90.6 | 0.06 | 22.9 | 5.7 | 32557 | -3 | 26 |
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 | 2.3 | 2.32 | 62.8 | 0.23 | 5.6 |
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 1OVD | 2.3 | 25 | 27913 | 1526 | 90.6 | 0.189 | 0.186 | 0.241 | RANDOM | 36.13 |
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] | |
6.63 | -0.68 | -4.28 | -2.67 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 7.047 |
r_scangle_it | 3.778 |
r_scbond_it | 2.294 |
r_angle_refined_deg | 1.687 |
r_mcangle_it | 1.505 |
r_angle_other_deg | 0.925 |
r_mcbond_it | 0.809 |
r_nbd_other | 0.234 |
r_nbd_refined | 0.216 |
r_symmetry_vdw_other | 0.215 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4818 |
Nucleic Acid Atoms | |
Solvent Atoms | 165 |
Heterogen Atoms | 85 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |