2GPS
Crystal Structure of the Biotin Carboxylase Subunit, E23R mutant, of Acetyl-CoA Carboxylase from Escherichia coli.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1DV1 | PDB ENTRY 1DV1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 8.5 | 294 | 0.1 M magnesium formate, 14% (w/v) PEG3350, 8% (v/v) glycerol, and 20 mM calcium chloride, pH 8.5, VAPOR DIFFUSION, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.926 | α = 90 |
b = 92.619 | β = 98.84 |
c = 86.598 | 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 4 | 2005-07-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4A | 0.97924 | NSLS | X4A |
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 | 2.8 | 30 | 97.7 | 0.064 | 16.1503 | 3 | 24249 | 23691 | -3 | -3 |
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 | 2.8 | 2.9 | 90.7 | 0.3 | 3.131 | 2.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 1DV1 | 2.8 | 30 | 22813 | 21174 | 1639 | 93.67 | 0.20551 | 0.2013 | 0.25979 | RANDOM | 45.208 |
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] | |
-3.26 | -0.06 | 4.55 | -1.31 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.957 |
r_dihedral_angle_4_deg | 19.201 |
r_dihedral_angle_3_deg | 18.409 |
r_dihedral_angle_1_deg | 5.629 |
r_scangle_it | 2.389 |
r_angle_refined_deg | 1.468 |
r_scbond_it | 1.437 |
r_mcangle_it | 1.196 |
r_mcbond_it | 0.679 |
r_symmetry_hbond_refined | 0.359 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6896 |
Nucleic Acid Atoms | |
Solvent Atoms | 67 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
COMO | phasing |