5XE2
Endoribonuclease from Mycobacterial species
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5XE3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 7 | 293 | 0.2M sodium malonate at pH 7.0 and 20% (w/v) polyethylene glycol 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.99 | 38.16 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.475 | α = 90 |
b = 65.548 | β = 90 |
c = 57.39 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | ADSC QUANTUM 315r | 2016-06-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PAL/PLS BEAMLINE 5C (4A) | 0.9795 | PAL/PLS | 5C (4A) |
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) | 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 | 2.01 | 30 | 97.5 | 0.146 | 0.157 | 0.054 | 5.1 | 7.9 | 7261 |
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 | 1.87 | 1.9 | 92.5 | 0.734 | 0.787 | 0.273 | 0.884 | 7.7 |
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 | 5XE3 | 2.01 | 30 | 6119 | 307 | 99.03 | 0.2046 | 0.2037 | 0.2227 | RANDOM | 23.868 |
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] | |
0.02 | -0.13 | 0.11 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.313 |
r_dihedral_angle_4_deg | 18.051 |
r_dihedral_angle_3_deg | 12.882 |
r_dihedral_angle_1_deg | 5.757 |
r_angle_refined_deg | 1.182 |
r_angle_other_deg | 0.874 |
r_chiral_restr | 0.06 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 801 |
Nucleic Acid Atoms | |
Solvent Atoms | 59 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
MOLREP | phasing |
HKL | data scaling |