4GEJ
N-terminal domain of VDUP-1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 295 | 0.1 M Hepes, 0.2 M Calcium Acetate, 10-12% PEG monomethyl ether 5000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.13 | 60.75 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 79.74 | α = 90 |
b = 178.81 | β = 113.32 |
c = 81.89 | 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 210r | mirrows | 2011-10-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 | 0.9537 | Australian Synchrotron | MX1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.9 | 46.71 | 99.5 | 0.075 | 0.075 | 18.5 | 7.2 | 46358 | 46358 | 97 |
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) | ||||||||||
1 | 2.9 | 3.06 | 98.8 | 0.665 | 0.665 | 2.9 | 6.9 | 6708 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.9 | 46 | 46358 | 44007 | 2320 | 99.42 | 0.224 | 0.224 | 0.212 | 0.2936 | RANDOM | 89.105 |
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] | |
2.36 | 0.2 | -3.57 | 1.37 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.664 |
r_dihedral_angle_4_deg | 23.069 |
r_dihedral_angle_3_deg | 22.804 |
r_dihedral_angle_1_deg | 8.533 |
r_angle_refined_deg | 1.817 |
r_chiral_restr | 0.107 |
r_bond_refined_d | 0.013 |
r_gen_planes_refined | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 10933 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 5 |
Software
Software | |
---|---|
Software Name | Purpose |
Blu-Ice | data collection |
MOLREP | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |