4C2L
Crystal structure of endo-xylogalacturonan hydrolase from Aspergillus tubingensis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1NHC | PDB ENTRIES 1NHC, 1RMG, 1CZF AND 2IQ7 |
experimental model | PDB | 1RMG | PDB ENTRIES 1NHC, 1RMG, 1CZF AND 2IQ7 |
experimental model | PDB | 1CZF | PDB ENTRIES 1NHC, 1RMG, 1CZF AND 2IQ7 |
experimental model | PDB | 2IQ7 | PDB ENTRIES 1NHC, 1RMG, 1CZF AND 2IQ7 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.4 | 298 | 2.9 M AMMONIUM SULFATE, 0.1 M NA-ACETATE BUFFER PH 4.4, VAPOR DIFFUSION, HANGING DROP, 298 K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.8 | 67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.44 | α = 90 |
b = 121.18 | β = 90 |
c = 129.67 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2010-02-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | ESRF | ID23-1 |
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 | 1.75 | 40.7 | 99.8 | 0.1 | 11.6 | 7.1 | 60896 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.75 | 1.84 | 100 | 0.58 | 3.7 | 7.2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 ENTRIES 1NHC, 1RMG, 1CZF AND 2IQ7 | 1.75 | 88.54 | 57809 | 3084 | 99.9 | 0.16846 | 0.16734 | 0.18927 | RANDOM | 20.587 |
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] | |
0.41 | -0.47 | 0.06 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.957 |
r_dihedral_angle_4_deg | 19.223 |
r_dihedral_angle_3_deg | 10.835 |
r_dihedral_angle_1_deg | 5.734 |
r_angle_refined_deg | 1.327 |
r_chiral_restr | 0.087 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2690 |
Nucleic Acid Atoms | |
Solvent Atoms | 458 |
Heterogen Atoms | 94 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |