4IXD
X-ray structure of lfa-1 i-domain in complex with ibe-667 at 1.8a resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1XDG |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 4.6 | 293 | 0.085M sodium acetate, pH4.6, 0.17M ammonium acetate, 15% glycerol and 25.5% (w/v) PEG4000 , VAPOR DIFFUSION, temperature 293.0K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.33 | 47.14 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 45.3 | α = 90 |
b = 65.9 | β = 90 |
c = 133.6 | γ = 90 |
Symmetry | |
---|---|
Space Group | I 2 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 293 | IMAGE PLATE | MAR scanner 345 mm plate | 2000-09-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM1A | 0.873 | ESRF | BM1A |
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 | 1.8 | 8 | 99 | 0.072 | 22.9 | 4.3 | 18740 | 18688 |
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) | |||||||||||
1 | 1.8 | 1.86 | 99 | 0.134 | 10.6 | 4.2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1XDG | 1.8 | 7.97 | 17770 | 17608 | 961 | 99.09 | 0.17295 | 0.17295 | 0.17155 | 0.19934 | RANDOM | 15.01 |
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] | |
0.03 | -0.04 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.69 |
r_dihedral_angle_4_deg | 17.097 |
r_dihedral_angle_3_deg | 11.554 |
r_dihedral_angle_1_deg | 5.564 |
r_scangle_it | 2.097 |
r_scbond_it | 1.211 |
r_angle_refined_deg | 0.973 |
r_mcangle_it | 0.684 |
r_mcbond_it | 0.341 |
r_chiral_restr | 0.07 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1468 |
Nucleic Acid Atoms | |
Solvent Atoms | 299 |
Heterogen Atoms | 33 |
Software
Software | |
---|---|
Software Name | Purpose |
MAR345dtb | data collection |
X-PLOR | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
X-PLOR | phasing |