3HR9
The truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase F40I mutant
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1ZM1 | PDB ENTRY 1ZM1 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | LIQUID DIFFUSION | 8.5 | 295 | 24% PEG5KMME, 0.5M calcium acetate, 0.35M Tris-HCl, pH8.5, LIQUID DIFFUSION, temperature 295K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.69 | 54.27 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 60.3 | α = 90 |
b = 68.03 | β = 90 |
c = 70.46 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 120 | IMAGE PLATE | RIGAKU RAXIS IV | 2006-11-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.54 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.7 | 27.77 | 95.7 | 0.044 | 62.2 | 11 | 32440 | 31160 | 1 | 21.5 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.7 | 1.76 | 100 | 0.347 | 9.6 | 10 | 3203 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1ZM1 | 1.7 | 27.77 | 32440 | 31160 | 3102 | 95.6 | 0.193 | 0.193 | 0.18 | 0.229 | 0.22 | RANDOM | 22.9 |
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] | |
-1.75 | 5.64 | -3.89 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 27.3 |
c_scangle_it | 2.74 |
c_scbond_it | 1.92 |
c_angle_deg | 1.8 |
c_mcangle_it | 1.68 |
c_mcbond_it | 1.15 |
c_improper_angle_d | 0.89 |
c_bond_d | 0.012 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1898 |
Nucleic Acid Atoms | |
Solvent Atoms | 242 |
Heterogen Atoms | 23 |
Software
Software | |
---|---|
Software Name | Purpose |
CrystalClear | data collection |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |