1J2R
Crystal structure of Escherichia coli gene product Yecd at 1.3 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 5.5 | 293 | MPD, TRIS, acetate, NaCl, Lysine, pH 5.5, EVAPORATION, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.03 | 39.06 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 140.502 | ¦Á = 90 |
b = 108.886 | ¦Â = 90 |
c = 50.419 | ¦Ã = 90 |
Symmetry | |
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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 | ADSC QUANTUM 4 | 2002-06-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.934 | ESRF | ID14-1 |
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 | 1.3 | 50.77 | 85.9 | 0.059 | 6.4 | 5.5 | 190258 | 163406 | 3 | 18.62 |
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 | 1.3 | 1.35 | 72.6 | 0.064 | 2.5 | 13256 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 entries 1NBA and 1IM5 | 1.3 | 50.77 | 162173 | 155206 | 8200 | 85.89 | 0.14596 | 0.14499 | 0.16494 | RANDOM | 11.354 |
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] | |
-0.5 | -0.03 | 0.53 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 5.611 |
r_scangle_it | 3.092 |
r_scbond_it | 1.926 |
r_angle_refined_deg | 1.399 |
r_mcangle_it | 1.263 |
r_angle_other_deg | 0.83 |
r_mcbond_it | 0.691 |
r_symmetry_vdw_other | 0.271 |
r_nbd_other | 0.253 |
r_nbd_refined | 0.224 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5751 |
Nucleic Acid Atoms | |
Solvent Atoms | 924 |
Heterogen Atoms | 96 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |
TRUNCATE | data scaling |
T-COFFEE | phasing |
MODELLER | phasing |
AMoRE | phasing |