3EVS
Crystal structure of the GDF-5:BMP receptor IB complex.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 5.25 | 294 | 0.1M sodium acetate, 50% PPG 400, 30mM magnesium sulfate, pH 5.25, VAPOR DIFFUSION, temperature 294K |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 76.455 | α = 90 |
b = 76.455 | β = 90 |
c = 82.784 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 42 21 2 |
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 | MARMOSAIC 225 mm CCD | mirrors | 2006-06-05 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | MARMOSAIC 225 mm CCD | mirrors | 2007-03-07 | M | MAD | |||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.10485 | SLS | X06SA |
2 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.97962, 0.97979, 0.90789 | BESSY | 14.1 |
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 | 2.1 | 34.19 | 99.5 | 0.071 | 9.66 | 15897 | 14815 |
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) | |||||||||||
1,2 | 2.1 | 2.18 | 100 | 0.354 | 5.3 | 9.87 | 1455 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 2.1 | 34.19 | 15897 | 14814 | 752 | 99.45 | 0.217 | 0.217 | 0.215 | 0.256 | RANDOM | 71.871 |
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] | |
-2.81 | -2.81 | 5.63 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.453 |
r_dihedral_angle_3_deg | 20.705 |
r_dihedral_angle_4_deg | 19.031 |
r_dihedral_angle_1_deg | 7.728 |
r_scangle_it | 3.996 |
r_scbond_it | 2.969 |
r_mcangle_it | 2.126 |
r_angle_refined_deg | 1.339 |
r_mcbond_it | 1.249 |
r_symmetry_vdw_refined | 0.357 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1483 |
Nucleic Acid Atoms | |
Solvent Atoms | 51 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
d*TREK | data scaling |
SHARP | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MAR345dtb | data collection |
CrystalClear | data reduction |
CrystalClear | data scaling |