6IQU
Crystal structure of Prc with PDZ domain deletion in complex with NlpI
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5WQL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 289 | PEG3350, sodium citrate tribasic dihydrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.97 | 58.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.827 | α = 90 |
b = 151.082 | β = 90 |
c = 148.38 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | 110 | CCD | RAYONIX MX300HE | LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator , A Pair of K-B Focusing Mirrors | 2018-09-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSRRC BEAMLINE TPS 05A | 0.99984 | NSRRC | TPS 05A |
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 | 2.9 | 50 | 95.9 | 0.057 | 0.088 | 0.042 | 18.95 | 4.4 | 25531 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.9 | 3 | 76 | 0.201 | 0.276 | 0.141 | 0.963 | 4.39 | 3.4 |
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 | 5WQL | 2.9 | 38.8 | 22490 | 1192 | 88.88 | 0.19398 | 0.1919 | 0.2334 | RANDOM | 49.792 |
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 |
r_dihedral_angle_2_deg | 32.855 |
r_dihedral_angle_4_deg | 20.457 |
r_dihedral_angle_3_deg | 19.522 |
r_long_range_B_refined | 10.693 |
r_long_range_B_other | 10.692 |
r_dihedral_angle_1_deg | 7.186 |
r_scangle_other | 7.118 |
r_mcangle_it | 7.082 |
r_mcangle_other | 7.081 |
r_scbond_it | 4.78 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6434 |
Nucleic Acid Atoms | |
Solvent Atoms | 11 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data scaling |
PHASER | phasing |
Coot | model building |
HKL-2000 | data reduction |