7O1F
PCNA from Chaetomium thermophilum in complex with PolD4 PIP peptide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7O1E |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 0.2 M Calcium acetate hydrate, 0.1 M Sodium cacodylate, pH 6.5, 36 % v/v PEG 300 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.54 | 51.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.891 | α = 60.94 |
b = 84.711 | β = 89.6 |
c = 84.89 | γ = 81.22 |
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 | CCD | RIGAKU SATURN 944+ | 2020-12-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54178 |
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 | 2.45 | 30.39 | 94.2 | 0.13 | 0.151 | 0.076 | 0.994 | 7.2 | 3.9 | 59727 |
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 | 2.45 | 2.52 | 92.1 | 1.368 | 1.61 | 0.841 | 0.406 | 3.6 |
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 | 7O1E | 2.45 | 30.39 | 56897 | 2829 | 94.16 | 0.2221 | 0.2202 | 0.2619 | RANDOM | 43.964 |
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] | |
1.51 | 0.94 | -2.29 | 1.3 | 0.95 | -0.67 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.16 |
r_dihedral_angle_4_deg | 20.746 |
r_dihedral_angle_3_deg | 16.553 |
r_dihedral_angle_1_deg | 7.773 |
r_angle_refined_deg | 1.461 |
r_angle_other_deg | 1.226 |
r_chiral_restr | 0.06 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11435 |
Nucleic Acid Atoms | |
Solvent Atoms | 160 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
Aimless | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |