4ZOE
Crystal Structure of beta-glucosidase from Listeria innocua
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1EX1 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 298 | PEG 4000, NaCl, LiSO4, glycerol |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.86 | 57.02 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 89.75 | α = 90 |
b = 95.1 | β = 96.34 |
c = 214.996 | γ = 90 |
Symmetry | |
---|---|
Space Group | I 1 2 1 |
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 210 | 2012-11-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 1.0 | Photon Factory | AR-NW12A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.8 | 28.38 | 98.5 | 8.2 | 4.9 | 163230 |
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 | 1EX1 | 1.8 | 28.17 | 154994 | 8215 | 98.28 | 0.183 | 0.1801 | 0.2398 | RANDOM | 14.86 |
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] | |
0.02 | 0.02 | -0.03 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.051 |
r_dihedral_angle_4_deg | 18.857 |
r_sphericity_free | 18.123 |
r_dihedral_angle_3_deg | 13.732 |
r_dihedral_angle_1_deg | 6.749 |
r_sphericity_bonded | 5.574 |
r_rigid_bond_restr | 4.595 |
r_angle_other_deg | 2.042 |
r_angle_refined_deg | 2.021 |
r_chiral_restr | 0.126 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 11190 |
Nucleic Acid Atoms | |
Solvent Atoms | 1173 |
Heterogen Atoms | 26 |
Software
Software | |
---|---|
Software Name | Purpose |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |