6PZJ
Structure of the N-terminal domain (residues 43-304) of Methyl-accepting chemotaxis protein from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Copenhageni (strain Fiocruz L1-130)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9.5 | 290 | RigakuReagents JCSG+ screen A7: 20% (w/V) PEG 8000, 100mM CHES / NaOH pH 9.5: LpinA.18975.a.B2.PW38653 at 19.51mg/ml: cryo: 20% EG in 2 steps: tray 310977 a7: puck hqx5-3. For phasing: Microlytic MCSG1 screen condition H3: 20% (w/V) PEG 3350, 200mM Lithium acetate: LpinA.18975.a.B2.PW38653 at 19.51mg/ml. A crystal from this condition was soaked for 15sec in a mix of 90% reservoir and 10% 2.5M NaI in EG, and for another 15sec in a mix of 80% reservoir and 20% 2.5M NaI in EG, and flash frozen for in-house data collection: tray 310978 h3: puck hqx5-12 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 72.09 | α = 90 |
b = 72.09 | β = 90 |
c = 116.89 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | RAYONIX MX-300 | 2019-07-18 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | 2019-07-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
2 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.75 | 38.416 | 100 | 0.046 | 0.048 | 1 | 30.66 | 11.48 | 31892 | 32.859 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.75 | 1.8 | 100 | 0.599 | 0.641 | 0.875 | 3.18 | 7.958 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | SAD | THROUGHOUT | 1.75 | 38.416 | 1.35 | 31821 | 1984 | 99.98 | 0.1677 | 0.1652 | 0.2053 | 0 | 32.9902 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.224 |
f_angle_d | 0.932 |
f_chiral_restr | 0.067 |
f_bond_d | 0.008 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2132 |
Nucleic Acid Atoms | |
Solvent Atoms | 223 |
Heterogen Atoms | 9 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |
PARROT | phasing |
ARP/wARP | model building |
Coot | model building |