5X7N
Crystal structure of meso-diaminopimelate decarboxylase (DAPDC) from Corynebacterium glutamicum
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5X7M |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | Sodium citrate tribasic, Sodium cacodylate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.65 | 53.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 114.543 | α = 90 |
b = 91.702 | β = 90 |
c = 95.161 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 270 | 2014-10-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PAL/PLS BEAMLINE 7A (6B, 6C1) | 0.97934 | PAL/PLS | 7A (6B, 6C1) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.72 | 95.17 | 95.2 | 40.23 | 5.9 | 95643 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.72 | 1.75 |
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 | 5X7M | 1.72 | 23.461 | 95643 | 5058 | 94.55 | 0.1725 | 0.1705 | 0.2112 | RANDOM | 18.718 |
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] | |
-0.19 | -0.36 | 0.55 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.196 |
r_dihedral_angle_4_deg | 11.914 |
r_dihedral_angle_3_deg | 10.981 |
r_dihedral_angle_1_deg | 6.301 |
r_angle_refined_deg | 2.124 |
r_angle_other_deg | 1.099 |
r_chiral_restr | 0.14 |
r_bond_refined_d | 0.022 |
r_gen_planes_refined | 0.012 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6618 |
Nucleic Acid Atoms | |
Solvent Atoms | 892 |
Heterogen Atoms | 98 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data collection |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
HKL-2000 | phasing |