4RSQ
2.9A resolution structure of SRPN2 (K198C/E359C) from Anopheles gambiae
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3PZF | PDB ENTRY 3PZF |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 6.9 | 293 | 1.0 M sodium phosphate monobasic monohydrate, potassium phosphate dibasic, pH 6.9, vapor diffusion, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.76 | 55.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 97.925 | α = 90 |
b = 164.392 | β = 90.02 |
c = 186.181 | 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 | PIXEL | DECTRIS PILATUS 6M | 2014-10-18 | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.0000 | APS | 17-ID |
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 | 2.9 | 47.82 | 99.5 | 0.135 | 7.9 | 3.4 | 129666 | 129666 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.9 | 2.95 | 99.8 | 0.635 | 0.418 | 2 | 3.3 | 6417 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | 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 ENTRY 3PZF | 2.9 | 47.82 | -3 | 129619 | 6285 | 99.34 | 0.1968 | 0.1939 | 0.2545 | RANDOM | 42.018 |
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] | |
-32.69 | 0.23 | 67.51 | -34.82 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.441 |
r_dihedral_angle_3_deg | 16.113 |
r_dihedral_angle_4_deg | 14.732 |
r_dihedral_angle_1_deg | 6.208 |
r_mcangle_it | 2.81 |
r_mcbond_it | 1.619 |
r_mcbond_other | 1.619 |
r_angle_refined_deg | 1.08 |
r_angle_other_deg | 0.71 |
r_chiral_restr | 0.064 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 33765 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
JDirector | data collection |
XDS | data reduction |