4IXN
Crystal Structure of Zn(II)-bound E37A,C66A,C67A triple mutant YjiA GTPase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 1.5 uL of 12.4 mg/mL triple mutant YjiA in 0.1 M NaCl, 1 mM TCEP, 25 mM HEPES, mixed with 0.3 uL 0.1 M CaCl2 and 1.5 uL 1.3 M ammonium sulfate, 0.1 M HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.03 | 39.44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.071 | α = 90 |
b = 68.436 | β = 104.23 |
c = 77.699 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | PIXEL | PSI PILATUS 6M | 2012-07-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.9795 | APS | 24-ID-C |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.05 | 75.3 | 98.5 | 0.085 | 18.6 | 6.5 | 35715 | 35715 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.05 | 2.09 | 98.8 | 0.59 | 2.9 | 5.7 | 1784 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.05 | 75.3 | 1.38 | 35309 | 35309 | 1747 | 98.31 | 0.2044 | 0.2027 | 0.2381 | same as for Zn(II)-soaked WT YjiA between 30 and 2.57 A resolution, random for remainder | 43.79 |
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 | 11.38 |
f_angle_d | 0.727 |
f_chiral_restr | 0.049 |
f_bond_d | 0.008 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4811 |
Nucleic Acid Atoms | |
Solvent Atoms | 256 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
APS | data collection |
PHENIX | model building |
PHENIX | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
PHENIX | phasing |