7LM3
Crystal Structure of Thr316Ala mutant of JAMM domain of S. pombe
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293.15 | 0.2 M ammonium phosphate dibasic (pH 8.0), 20% w/v polyethylene glycol 3,350 with 40% v/v Polypropylene glycol P400 as an additive |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.77 | 55.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.531 | α = 90 |
b = 121.338 | β = 129.581 |
c = 57.145 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | IMAGE PLATE | MAR scanner 300 mm plate | 2015-08-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 1.033 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.7 | 50 | 98.8 | 0.074 | 0.086 | 0.043 | 9 | 3.9 | 12793 |
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 | 2.7 | 2.75 | 97.5 | 0.721 | 0.838 | 0.425 | 0.786 | 3.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4JXE | 2.7 | 44.04 | 1.4 | 12785 | 624 | 98.62 | 0.2033 | 0.2006 | 0.2529 | 66.42 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 6.9164 |
f_angle_d | 1.1392 |
f_chiral_restr | 0.0579 |
f_bond_d | 0.0097 |
f_plane_restr | 0.0094 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2812 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
MOLREP | phasing |