8B7X
X-ray structure of the CeuE Homologue from Geobacillus stearothermophilus - apo form.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3ZKW |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | Index D3: 0.1M HEPES, pH 7.0, 30% Jeffamine ED 2001, pH 7.0. No cryo. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
26.11 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 32.519 | α = 81.566 |
b = 35.725 | β = 83.242 |
c = 52.29 | γ = 65.06 |
Symmetry | |
---|---|
Space Group | P 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 | PIXEL | DECTRIS PILATUS3 6M | 2018-11-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97622 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.42 | 32.225 | 94.9 | 0.033 | 0.046 | 0.033 | 0.998 | 5.8 | 2 | 37722 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.42 | 1.44 | 0.323 | 0.457 | 0.323 | 0.862 | 1.7 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3zkw | 1.42 | 32.225 | 37657 | 1940 | 94.67 | 0.169 | 0.1655 | 0.2281 | 28.729 |
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] | |
0.43 | 0.076 | 1.675 | -0.664 | -1.253 | 0.549 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 15.887 |
r_dihedral_angle_6_deg | 15.737 |
r_dihedral_angle_2_deg | 9.768 |
r_lrange_other | 7.156 |
r_lrange_it | 7.152 |
r_scangle_it | 6.871 |
r_scangle_other | 6.469 |
r_dihedral_angle_1_deg | 6.4 |
r_scbond_it | 6.227 |
r_rigid_bond_restr | 6.212 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2174 |
Nucleic Acid Atoms | |
Solvent Atoms | 56 |
Heterogen Atoms | 24 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
REFMAC | refinement |
Aimless | data scaling |
DIALS | data reduction |
MOLREP | phasing |