2VWS
Crystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1DXE | PDB ENTRY 1DXE |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 6.5 | WRIGHT, A., BLEWETT, A., FULOP, V., COOPER, R., BURROWS, S., JONES, C. & ROPER, D. (2002). EXPRESSION, PURIFICATION, CRYSTALLIZATION AND PRELIMINARY CHARACTERIZATION OF AN HHED ALDOLASE HOMOLOGUE FROM ESCHERICHIA COLI K12. ACTA CRYST. D58, 2191-2193., pH 6.5 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.5 | 47 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 105.2 | α = 90 |
b = 136.8 | β = 90 |
c = 123.2 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 2 2 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 | ADSC CCD | MIRRORS | 2002-06-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX14.2 | SRS | PX14.2 |
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 | 1.39 | 60 | 99.5 | 0.06 | 27.2 | 4.3 | 176395 | -3 | 18.8 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.39 | 1.44 | 99.3 | 0.4 | 2.1 | 3.3 |
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 | PDB ENTRY 1DXE | 1.39 | 59.76 | 169354 | 7041 | 99.5 | 0.172 | 0.171 | 0.191 | RANDOM | 23.74 |
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] | |
0.62 | -0.1 | -0.52 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.943 |
r_dihedral_angle_3_deg | 12.867 |
r_dihedral_angle_4_deg | 10.941 |
r_dihedral_angle_1_deg | 5.848 |
r_scangle_it | 3.635 |
r_scbond_it | 2.437 |
r_mcangle_it | 1.672 |
r_angle_refined_deg | 1.599 |
r_mcbond_it | 1.12 |
r_nbd_refined | 0.206 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5853 |
Nucleic Acid Atoms | |
Solvent Atoms | 959 |
Heterogen Atoms | 32 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |