8HPC
Crystal structure of C171A Mutant of N-carbamyl-D-amino acid amidohydrolase complexed with N-carbamyl-D-Hydroxyphenylglycine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | PEG3350, BIS-TRIS, Ammonium acetate, calcium chloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.07 | 40.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.165 | α = 91.4 |
b = 79.865 | β = 98.48 |
c = 91.07 | γ = 92.78 |
Symmetry | |
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Space Group | P 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 | Bruker PHOTON II | 2022-03-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | BRUKER D8 QUEST | 1.54184 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.52 | 46.59 | 98 | 0.14 | 7.3 | 3 | 72971 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.52 | 2.57 | 0.433 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.52 | 46.59 | 69433 | 3537 | 98.04 | 0.21987 | 0.2181 | 0.25324 | RANDOM | 22.847 |
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] | |
-11.65 | -3.22 | -11.71 | -3.9 | -0.58 | 15.55 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.839 |
r_dihedral_angle_4_deg | 18.596 |
r_dihedral_angle_3_deg | 14.813 |
r_dihedral_angle_1_deg | 7.568 |
r_long_range_B_refined | 4.871 |
r_long_range_B_other | 4.856 |
r_scangle_other | 3.111 |
r_mcangle_it | 3.074 |
r_mcangle_other | 3.074 |
r_scbond_it | 2.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 19127 |
Nucleic Acid Atoms | |
Solvent Atoms | 270 |
Heterogen Atoms | 120 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |