3V4D
Crystal structure of RutC protein a member of the YjgF family from E.coli
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4 | 293 | 0.1 M MMT, 30% PEG 1500, +xylitol, K/Na tartrate, 2,6-pyridinecarboxylic acid, 2,4-pyridinecarboxylic acid, 2,5-pyridinecarboxylic acid, 4-pyridazine carboxylic acid, 3-sulfobenzoic acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.13 | 42.27 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 92.255 | α = 90 |
b = 179.181 | β = 90 |
c = 45.217 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 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 | 2010-11-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.9787 | APS | 21-ID-F |
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 | 1.95 | 50 | 99.9 | 0.094 | 0.094 | 34.3 | 9.6 | 55593 | 55593 | -3 | 28.6 |
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 | 1.95 | 1.98 | 100 | 0.633 | 0.633 | 3 | 9 | 2712 |
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 | SAD | THROUGHOUT | 1.95 | 50 | 52607 | 52607 | 2816 | 99.69 | 0.1946 | 0.1946 | 0.19337 | 0.21658 | RANDOM | 43.366 |
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] | |
-0.43 | -3.17 | 3.6 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.923 |
r_dihedral_angle_4_deg | 14.983 |
r_dihedral_angle_3_deg | 12.056 |
r_dihedral_angle_1_deg | 6.543 |
r_angle_other_deg | 2.395 |
r_angle_refined_deg | 1.707 |
r_chiral_restr | 0.104 |
r_bond_refined_d | 0.018 |
r_gen_planes_refined | 0.01 |
r_gen_planes_other | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5642 |
Nucleic Acid Atoms | |
Solvent Atoms | 342 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
MD2 | data collection |
HKL-3000 | phasing |
SHELXCD | phasing |
SHELXE | model building |
MLPHARE | phasing |
DM | model building |
ARP/wARP | model building |
SOLVE | phasing |
RESOLVE | model building |
CCP4 | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
DM | phasing |
RESOLVE | phasing |
CCP4 | phasing |