8H1A
Crystal structure of MnmM from S. aureus in apo state (1.44 A)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.68 | 54.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.494 | α = 90 |
b = 63.91 | β = 90 |
c = 135.044 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | DECTRIS EIGER X 9M | 2022-06-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PAL/PLS BEAMLINE 5C (4A) | 0.97965 | PAL/PLS | 5C (4A) |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 1.44 | 47.34 | 95.5 | 0.073 | 0.076 | 0.021 | 0.999 | 17.1 | 13.3 | 67371 | 20.9 |
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 | 1.44 | 1.54 | 66.5 | 1.955 | 2.025 | 0.525 | 0.605 | 1.5 | 14.8 |
Refinement
Statistics | |||||||||||||||||||
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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 | MOLECULAR REPLACEMENT | THROUGHOUT | AlphaFold model (UniProt: Q2FXG9) | 1.44 | 47.34 | 63959 | 3409 | 84.1 | 0.15394 | 0.15185 | 0.19218 | RANDOM | 26.467 |
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] | |
-1.05 | -0.29 | 1.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.636 |
r_dihedral_angle_4_deg | 15.031 |
r_dihedral_angle_3_deg | 12.328 |
r_dihedral_angle_1_deg | 6.467 |
r_long_range_B_refined | 4.411 |
r_long_range_B_other | 4.021 |
r_scangle_other | 3.322 |
r_mcangle_it | 2.835 |
r_mcangle_other | 2.826 |
r_scbond_it | 2.679 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2860 |
Nucleic Acid Atoms | |
Solvent Atoms | 307 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
MxDC | data collection |
STARANISO | data scaling |
XDS | data reduction |
MOLREP | phasing |
Coot | model building |
REFMAC | refinement |
PDB_EXTRACT | data extraction |