6U3L
Crystal structure of Hemerythrin HHE cation binding domain-containing protein: Rv2633c homolog from Mycobacterium kansasii
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 290 | MCSG-1 screen F3: 200mM ammonium citrate, 25% PEG 3350: MykaA.20209.a.B11.PB00101 at 2mg/ml, grown at 14C: cryo: 20% EG: tray 308332F3: puck vlf8-4. For experimental phasing, a crystal from MCSG-1 screen, condition F3 (200mM ammonium citrate, 25% PEG 3350) with MykaA.20209.a B1.PB00101 at 3mg/ml, grown at 14C, was incubated for 15 sec each in a solution of 90% reservoir and 10% 2.5M sodium iodide in ethylene glycol, and then in a solution of 80% reservoir and 20% 2.5M sodium iodide in ethylene glycol, and vitrified in liquid nitrogen: tray 308326f3: puck fdn8-5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41.45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.05 | α = 90 |
b = 52.05 | β = 90 |
c = 104.7 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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 | 2010-03-21 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | 2010-03-18 | 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 | 50 | 100 | 0.041 | 0.044 | 1 | 24.94 | 6.91 | 17189 | 28.21 |
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 | 99.9 | 0.639 | 0.716 | 0.85 | 2.18 | 4.944 |
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 | FREE R-VALUE | 1.75 | 45.08 | 1.35 | 17176 | 1695 | 99.89 | 0.1819 | 0.178 | 0.2179 | 0 | 36.05 |
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 | 13.9897 |
f_angle_d | 0.8509 |
f_chiral_restr | 0.0483 |
f_bond_d | 0.0079 |
f_plane_restr | 0.0065 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1266 |
Nucleic Acid Atoms | |
Solvent Atoms | 118 |
Heterogen Atoms | 4 |
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 |