2GED
Signal Recognition Particle Receptor Beta-Subunit in nucleotide-free dimerized form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | MICROBATCH UNDER PARAFFIN OIL | 5.5 | 277 | 1.3M ammonium sulfate, 50mM Bis/Tris/HCl, 0.5mM GDP, 5mM magnesium chloride, 5mM Hepes, 125mM sodium chloride, 2.5mM DTT, 0.25mM EDTA, pH 5.5, MICROBATCH UNDER PARAFFIN OIL, temperature 277K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.99 | 58.91 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 74.996 | α = 90 |
b = 74.996 | β = 90 |
c = 158.475 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 61 |
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 | MAR CCD 165 mm | 2003-11-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X9A | 1.00944 | NSLS | X9A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 33.8 | 98.6 | 0.074 | 24.2 | 5.6 | 33853 | 33373 | 1 | 49.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1NRJ chain B | 2.2 | 25 | 2 | 25288 | 22942 | 2527 | 99.75 | 0.223 | 0.18832 | 0.18264 | 0.23941 | RANDOM | 38.144 |
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] | |
1.76 | 0.88 | 1.76 | -2.64 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.851 |
r_dihedral_angle_4_deg | 23.28 |
r_dihedral_angle_3_deg | 18.004 |
r_dihedral_angle_1_deg | 6.729 |
r_scangle_it | 4.815 |
r_scbond_it | 3.301 |
r_mcangle_it | 2.331 |
r_angle_refined_deg | 1.894 |
r_mcbond_it | 1.641 |
r_angle_other_deg | 1.086 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2591 |
Nucleic Acid Atoms | |
Solvent Atoms | 294 |
Heterogen Atoms | 30 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
BEAST | phasing |