3IOS
Structure of MTB dsbF in its mixed oxidized and reduced forms
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1LU4 | PDB ENTRY 1LU4 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 7 | 298 | 0.1 M NA malonate ph 7.0, 2.04 M NA citrate, 5% LDAO, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.12 | α = 90 |
b = 100.12 | β = 90 |
c = 30.09 | γ = 90 |
Symmetry | |
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Space Group | P 42 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 200 | CCD | ADSC QUANTUM 4 | 2003-07-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | ALS | 8.2.2 |
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 | 1.6 | 50 | 100 | 0.068 | 40.68 | 23073 | 1 |
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) | |||||||||||
1.6 | 1.66 | 100 | 0.597 | 3.85 |
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 | AB INITIO | FREE R | PDB ENTRY 1LU4 | 1.6 | 10 | 16851 | 2036 | 90 | 0.144 | 0.144 | 0.2 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
233 | 1130 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.094 |
s_similar_adp_cmpnt | 0.06 |
s_non_zero_chiral_vol | 0.051 |
s_zero_chiral_vol | 0.049 |
s_angle_d | 0.034 |
s_anti_bump_dis_restr | 0.033 |
s_from_restr_planes | 0.022 |
s_bond_d | 0.009 |
s_rigid_bond_adp_cmpnt | 0.003 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1025 |
Nucleic Acid Atoms | |
Solvent Atoms | 108 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
EPMR | phasing |
SHELXL | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |