4C1S
Glycoside hydrolase family 76 (mannosidase) Bt3792 from Bacteroides thetaiotaomicron VPI-5482
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3K7X | PDB ENTRY 3K7X |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | BT3792 AT A 20 MG PER ML BUFFERED IN IN 25 MM TRIS-HCL (PH 8.0), 500 MM NACL, 2 MM DTT WITH A RESERVOIR SOLUTION CONSISTING OF 5% GLYCEROL (V/V), 24% (W PER V) POLYETHYLENE GLYCOL 2,000 MONOMETHYL ETHER, 0.25 M SODIUM ACETATE, AND BIS-TRIS-HCL (PH 5.5) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.1 | α = 90 |
b = 44.42 | β = 101.43 |
c = 103.05 | 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 | MARRESEARCH MX-300HE | COLLIMATING MIRROR WITH TWO STRIPES (SI, RH AND PT) , TOROIDAL FOCUSING MIRROR (RH AND PT) | 2012-09-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | CLSI | 08ID-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 | 2.1 | 48 | 99.9 | 0.11 | 10.4 | 4.2 | 52497 |
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 | 2.1 | 2.21 | 99.9 | 0.48 | 3.3 | 4.2 |
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 3K7X | 2.1 | 48.03 | 49817 | 2674 | 99.83 | 0.2156 | 0.21359 | 0.25264 | RANDOM | 24.111 |
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] | |
12.47 | -21.1 | -13.73 | 1.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.243 |
r_dihedral_angle_4_deg | 19.648 |
r_dihedral_angle_3_deg | 15.706 |
r_dihedral_angle_1_deg | 7.162 |
r_mcangle_it | 3.252 |
r_scbond_it | 3.071 |
r_mcbond_it | 2.425 |
r_angle_refined_deg | 1.597 |
r_chiral_restr | 0.117 |
r_bond_refined_d | 0.014 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6078 |
Nucleic Acid Atoms | |
Solvent Atoms | 287 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
AutoProcess | data reduction |
SCALA | data scaling |
PHASER | phasing |