3MX0
Crystal Structure of EphA2 ectodomain in complex with ephrin-A5
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.8 | 298 | 20% PEG 3350, 200 mM Ammonium Citrate, 100 mM Na Citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
4.14 | 70.28 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 57.859 | α = 90 |
b = 89.049 | β = 96.22 |
c = 198.15 | γ = 90 |
Symmetry | |
---|---|
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 | CCD | ADSC QUANTUM 315 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.98792 | APS | 24-ID-C |
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 | 3.5 | 50 | 91.4 | 0.104 | 8.8 | 5.4 | 23143 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
3.5 | 3.63 | 71.1 | 0.219 | 0.22 | 6.2 | 5.2 |
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 (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 3.506 | 45.028 | 0.16 | 23129 | 22383 | 1123 | 88.12 | 0.2369 | 0.2338 | 0.2278 | 0.2951 | 0.2954 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
-20.6855 | 2.415 | 78.283 | -57.5975 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 20.55 |
f_angle_d | 1.472 |
f_chiral_restr | 0.093 |
f_bond_d | 0.01 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 8462 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 112 |
Software
Software | |
---|---|
Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
PHENIX | phasing |