6CWX
Crystal structure of human ribonuclease P/MRP proteins Rpp20/Rpp25
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 291.15 | 100 mM potassium formate, pH 7.5, 300 mM magnesium sulfate, 4.5% PEG 300, 4.5% PEG 400, 4.5% PEG 1000, 4.5% PEG 4000, and 4.5% PEG 8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.42 | 63.93 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 182.19 | α = 90 |
b = 182.19 | β = 90 |
c = 182.19 | γ = 90 |
Symmetry | |
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Space Group | I 4 3 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 | 100 | CCD | MARMOSAIC 225 mm CCD | 2015-06-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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 | 2.25 | 48.69 | 100 | 0.083 | 0.087 | 0.028 | 0.999 | 16.4 | 9.7 | 24742 |
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 | 2.25 | 2.32 | 100 | 0.495 | 0.523 | 0.165 | 0.924 | 4.7 | 9.8 |
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 | SIRAS | THROUGHOUT | 2.25 | 48.69 | 23502 | 1211 | 99.93 | 0.2143 | 0.2134 | 0.2322 | RANDOM | 54.096 |
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 | 31.779 |
r_dihedral_angle_4_deg | 13.925 |
r_dihedral_angle_3_deg | 13.032 |
r_dihedral_angle_1_deg | 5.477 |
r_angle_refined_deg | 1.384 |
r_angle_other_deg | 0.866 |
r_chiral_restr | 0.076 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1746 |
Nucleic Acid Atoms | |
Solvent Atoms | 100 |
Heterogen Atoms | 16 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
Aimless | data scaling |
autoSHARP | phasing |
BUCCANEER | model building |
PDB_EXTRACT | data extraction |