4BQ1
Crystal structure of of LamAcat from Zobellia galactanivorans
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3ILN | PDB ENTRY 3ILN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.2 | 277 | MONO-CRYSTALS WERE GROWN AT 4 DEGREE CELSIUS IN HANGING DROPS COMPOSED OF 2 MICROL OF ENZYME AT 10 MG.ML-1 AND 2 MICROL OF RESERVOIR SOLUTION CONTAINING 24% PEG 3350 AND 100 MM NA CITRATE PH 5.2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.559 | α = 90 |
b = 76.564 | β = 90 |
c = 142.119 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 315r | 2010-05-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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 | 1.45 | 47.37 | 99.7 | 0.1 | 11 | 6.3 | 86903 |
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 | 1.45 | 1.53 | 99.7 | 0.46 | 3.5 | 5.7 |
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 3ILN | 1.5 | 71.06 | 74179 | 3929 | 99.14 | 0.139 | 0.13752 | 0.1664 | RANDOM | 18.139 |
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] | |
1.36 | -0.4 | -0.96 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.541 |
r_dihedral_angle_4_deg | 27.51 |
r_sphericity_free | 19.255 |
r_dihedral_angle_3_deg | 12.705 |
r_sphericity_bonded | 11.66 |
r_rigid_bond_restr | 9.749 |
r_dihedral_angle_1_deg | 7.534 |
r_angle_refined_deg | 2.29 |
r_chiral_restr | 0.242 |
r_bond_refined_d | 0.028 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4050 |
Nucleic Acid Atoms | |
Solvent Atoms | 526 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |