4H17
Crystal structure of an isochorismatase (PP1826) from Pseudomonas putida KT2440 at 1.60 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 277 | 0.200M (NH4)2SO4, 20.00% PEG-3350, No Buffer pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.19 | 43.81 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 49.169 | α = 90 |
b = 49.348 | β = 90 |
c = 156.593 | 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 325 mm CCD | double crystal monochromator | 2009-07-31 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.91837,0.97925,0.97910 | SSRL | BL9-2 |
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 | 1.6 | 28.973 | 99.8 | 0.038 | 19.7 | 3.81 | 51103 | -3 | 16.915 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.6 | 1.64 | 100 | 0.536 | 0.536 | 0.624 | 2.4 | 3.83 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.6 | 28.973 | 51033 | 2586 | 98.87 | 0.1367 | 0.1357 | 0.1564 | RANDOM + TWIN LAW | 18.6092 |
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 | 5.06 | -2.25 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.18 |
r_dihedral_angle_4_deg | 18.953 |
r_dihedral_angle_3_deg | 12.05 |
r_dihedral_angle_1_deg | 6.219 |
r_angle_refined_deg | 1.6 |
r_angle_other_deg | 1.206 |
r_chiral_restr | 0.094 |
r_bond_refined_d | 0.013 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2957 |
Nucleic Acid Atoms | |
Solvent Atoms | 442 |
Heterogen Atoms | 42 |
Software
Software | |
---|---|
Software Name | Purpose |
MolProbity | model building |
PDB_EXTRACT | data extraction |
SHELX | phasing |
SHARP | phasing |
XSCALE | data scaling |
REFMAC | refinement |
XDS | data reduction |
SHELXD | phasing |