7AM7
Crystal structure of Peptiligase mutant - M222P/L217H/A225N/F189W/N218D
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7AM3 | D_1292111488 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 294 | 1.2 M Ammonium sulfate, 0.25 PEG3350, 0.1 M MES |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3 | 59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.798 | α = 90 |
b = 105.798 | β = 90 |
c = 191.516 | γ = 90 |
Symmetry | |
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Space Group | P 41 2 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 | IMAGE PLATE | MARRESEARCH | 2018-11-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR-H | 1.5418 |
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) | 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 | 2.61 | 48.61 | 99.8 | 0.263 | 0.281 | 0.099 | 0.99 | 8.3 | 8 | 33957 |
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 | 2.61 | 2.72 | 98.8 | 0.994 | 1.066 | 0.381 | 0.583 | 7.5 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | D_1292111488 | 2.61 | 48.59 | 32234 | 1661 | 99.78 | 0.1975 | 0.1955 | 0.2373 | RANDOM | 40.479 |
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] | |
1.17 | 1.17 | -2.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.845 |
r_dihedral_angle_3_deg | 15.73 |
r_dihedral_angle_4_deg | 11.96 |
r_dihedral_angle_1_deg | 6.798 |
r_angle_refined_deg | 1.559 |
r_angle_other_deg | 1.326 |
r_chiral_restr | 0.065 |
r_bond_refined_d | 0.009 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5702 |
Nucleic Acid Atoms | |
Solvent Atoms | 143 |
Heterogen Atoms | 89 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |