3LX1
Crystal Structure analysis of PCNA1 from Thermococcus kodakaraensis tk0535
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 295 | 2.4-2.8 M ammonium sulfate, 100 mM sodium citrate, 5-10% 2,4-methyl pentanediol. The protein solution has 10% glycerol, VAPOR DIFFUSION, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 50.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.23 | α = 90 |
b = 89.23 | β = 90 |
c = 62.67 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | RIGAKU RAXIS IV++ | 2009-08-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.54 |
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 | 29.21 | 99.8 | 0.094 | 7.9 | 5.57 | 19294 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.07 | 99.2 | 0.516 | 2.2 | 5.43 | 1920 |
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 | 29.21 | 19035 | 939 | 98.55 | 0.202 | 0.199 | 0.262 | RANDOM | 33.664 |
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] | |
0.72 | 0.36 | 0.72 | -1.08 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.787 |
r_dihedral_angle_4_deg | 18.612 |
r_dihedral_angle_3_deg | 16.764 |
r_dihedral_angle_1_deg | 6.489 |
r_scangle_it | 5.814 |
r_scbond_it | 3.454 |
r_mcangle_it | 2.207 |
r_angle_refined_deg | 1.771 |
r_mcbond_it | 1.202 |
r_chiral_restr | 0.128 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1956 |
Nucleic Acid Atoms | |
Solvent Atoms | 81 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data reduction |