6RS6
X-ray crystal structure of LsAA9B
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3EJA |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 294 | 20%(w/v) Polyethylene glycol monomethyl ether 500 10%(w/v) Polyethylene glycol 20.000 0.1 M Imidazole/MES (pH6.5) 0.02 M Glutamate, Alanine, Glycine, Lysine, and Serine (some racemic). |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.16 | 42.94 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 35.19 | α = 90 |
b = 72.48 | β = 90 |
c = 78.56 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
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 | 2014-02-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I911-3 | 0.9900 | MAX II | I911-3 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | 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 | 1.6 | 20 | 99.6 | 0.108 | 0.998 | 14.07 | 7.83 | 27139 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.6 | 1.7 | 98.5 | 0.678 | 0.764 | 2.74 | 6.01 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3EJA | 1.6 | 19.93 | 25765 | 1384 | 99.6 | 0.13903 | 0.1367 | 0.18219 | RANDOM | 16.406 |
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] | |
-0.41 | 0.26 | 0.15 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.843 |
r_dihedral_angle_4_deg | 19.195 |
r_dihedral_angle_3_deg | 10.468 |
r_sphericity_bonded | 9.553 |
r_dihedral_angle_1_deg | 6.495 |
r_rigid_bond_restr | 4.561 |
r_long_range_B_refined | 2.613 |
r_long_range_B_other | 2.612 |
r_scangle_other | 2.052 |
r_scbond_it | 1.52 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1640 |
Nucleic Acid Atoms | |
Solvent Atoms | 215 |
Heterogen Atoms | 76 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
MxCuBE | data collection |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |
Coot | model building |