1RWG
Crystal structure of Arthrobacter aurescens chondroitin AC lyase in complex with chondroitin tetrasaccharide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1RW9 | PDB entry 1RW9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.4 | PEG 8000, ammonium acetate, glycerol, phosphate buffer, 10 minutes soaking time, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.41 | 48.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.683 | α = 90 |
b = 86.449 | β = 106.87 |
c = 80.566 | 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 | 2002-06-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X8C | 0.9787 | NSLS | X8C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.5 | 50 | 99.9 | 0.077 | 9.2 | 3.8 | 120769 | 1 | 1 |
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 | 1.5 | 1.55 | 99.9 |
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 1RW9 | 1.5 | 28.06 | 119480 | 119480 | 1221 | 100 | 0.13664 | 0.13629 | 0.17267 | RANDOM | 18.336 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.55 | 0.33 | -0.31 | -0.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.33 |
r_dihedral_angle_4_deg | 13.834 |
r_dihedral_angle_3_deg | 11.059 |
r_sphericity_free | 6.262 |
r_dihedral_angle_1_deg | 6.1 |
r_sphericity_bonded | 5.558 |
r_scangle_it | 4.291 |
r_scbond_it | 3.186 |
r_mcangle_it | 2.47 |
r_angle_refined_deg | 1.832 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5600 |
Nucleic Acid Atoms | |
Solvent Atoms | 1061 |
Heterogen Atoms | 66 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |