4A64
Crystal structure of the N-terminal domain of human Cul4B at 2.57A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1U6G | PDB ENTRIES 1U6G, 1LDK, 1LDJ, 2HYE |
experimental model | PDB | 1LDK | PDB ENTRIES 1U6G, 1LDK, 1LDJ, 2HYE |
experimental model | PDB | 1LDJ | PDB ENTRIES 1U6G, 1LDK, 1LDJ, 2HYE |
experimental model | PDB | 2HYE | PDB ENTRIES 1U6G, 1LDK, 1LDJ, 2HYE |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 24% PEG4000, 100 MM LISO4, 100 MM TRIS (PH 8.2) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.79 | 55.92 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.248 | α = 90 |
b = 157.091 | β = 95.71 |
c = 92.916 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC CCD | 2011-08-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | Diamond | I02 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.57 | 19.97 | 99.7 | 0.06 | 18.6 | 4.2 | 58043 | 2 | 67 |
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 | 2.57 | 2.71 | 99.9 | 0.73 | 2 | 4.3 |
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 | PDB ENTRIES 1U6G, 1LDK, 1LDJ, 2HYE | 2.57 | 19.74 | 55064 | 2940 | 99.63 | 0.1866 | 0.18431 | 0.22989 | RANDOM | 51.113 |
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] | |
2.7 | -1.54 | -0.56 | -2.45 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.765 |
r_dihedral_angle_4_deg | 20.331 |
r_dihedral_angle_3_deg | 16.428 |
r_dihedral_angle_1_deg | 5.142 |
r_angle_refined_deg | 1.6 |
r_angle_other_deg | 1.414 |
r_chiral_restr | 0.082 |
r_bond_refined_d | 0.014 |
r_bond_other_d | 0.007 |
r_gen_planes_refined | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11036 |
Nucleic Acid Atoms | |
Solvent Atoms | 253 |
Heterogen Atoms | 28 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |