4FLA
Crystal structure of human RPRD1B, carboxy-terminal domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.5 | 291 | 25% PEG-3350, 0.2M ammonium acetate, 0.1M HEPES, pH 7.5, vapor diffusion, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.1 | 60.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.221 | α = 90 |
b = 100.221 | β = 90 |
c = 142.887 | γ = 90 |
Symmetry | |
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Space Group | P 4 21 2 |
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 | CCD | ADSC QUANTUM 315 | 2012-02-24 | M | SINGLE WAVELENGTH | |||||||
2 | 1 | x-ray | CCD | MARMOSAIC 300 mm CCD | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97931 | APS | 19-ID |
2 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.97944 | APS | 23-ID-B |
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 | 2.2 | 47.63 | 99.98 | 0.116 | 15.5351 | 9.62 | 37701 |
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 | 2.2 | 2.32 | 100 | 0.93 | 9.81 | 5387 |
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 | SAD | THROUGHOUT | 2.2 | 40 | 37678 | 1587 | 99.867 | 0.233 | 0.2316 | 0.2575 | thin shells (sftools) | 44.226 |
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] | |
1.791 | 1.791 | -3.583 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.544 |
r_dihedral_angle_3_deg | 14.351 |
r_dihedral_angle_4_deg | 13.181 |
r_dihedral_angle_1_deg | 4.173 |
r_angle_other_deg | 1.326 |
r_angle_refined_deg | 1.311 |
r_chiral_restr | 0.066 |
r_bond_refined_d | 0.013 |
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 | 3871 |
Nucleic Acid Atoms | |
Solvent Atoms | 148 |
Heterogen Atoms | 7 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
SHELX | phasing |
RESOLVE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |