3KX2
Crystal structure of Prp43p in complex with ADP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.75 | 277 | 100mM Mes-NaOH, pH 6.75, 14% PEG 8000, 300mM NaOAc, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.91 | 57.79 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 118.152 | α = 90 |
b = 118.152 | β = 90 |
c = 253.601 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 32 2 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 | PSI PILATUS 6M | 2009-08-07 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | MARMOSAIC 225 mm CCD | 2009-09-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 0.980 | SLS | X06SA |
2 | SYNCHROTRON | MAX II BEAMLINE I911-3 | 0.9795 | MAX II | I911-3 |
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 | 2.2 | 50 | 99.5 | 0.012 | 4.2 | 104963 | 104418 | -3 |
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) | |||||||||||
2.2 | 2.3 | 99.6 | 0.75 | 4.1 | 12891 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | SAD | 2.2 | 48.423 | 1.17 | 104963 | 104407 | 9826 | 98.01 | 0.2085 | 0.2085 | 0.2063 | 0.2497 | RANDOM | 53.766 |
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] | |
-3.601 | -3.601 | 5.868 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.966 |
f_angle_d | 1.013 |
f_chiral_restr | 0.072 |
f_bond_d | 0.006 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 12134 |
Nucleic Acid Atoms | |
Solvent Atoms | 982 |
Heterogen Atoms | 56 |
Software
Software | |
---|---|
Software Name | Purpose |
SHELXS | phasing |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |