3FMC
CRYSTAL STRUCTURE OF a putative succinylglutamate desuccinylase / aspartoacylase family protein (SAMA_0604) FROM SHEWANELLA AMAZONENSIS SB2B AT 1.80 A RESOLUTION
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | NANODROP, 1.5M Li2SO4, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.42 | 63.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 98.279 | α = 90 |
b = 140.101 | β = 90 |
c = 164.17 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | Adjustable focusing mirrors in K-B geometry | 2008-10-11 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.94645, 0.97967 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.8 | 29.735 | 88.4 | 0.105 | 0.105 | 5.074 | 4.8 | 184530 | 18.527 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.8 | 1.85 | 69.7 | 0.572 | 0.572 | 1.3 | 3.6 | 10674 |
Refinement
Statistics | |||||||||||||||||||
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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 | 1.8 | 29.735 | 184450 | 9270 | 88.15 | 0.157 | 0.155 | 0.187 | RANDOM | 22.582 |
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] | |
0.22 | -0.4 | 0.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 25.907 |
r_dihedral_angle_4_deg | 12.192 |
r_dihedral_angle_3_deg | 10.879 |
r_scangle_it | 6.346 |
r_scbond_it | 4.743 |
r_dihedral_angle_1_deg | 4.608 |
r_mcangle_it | 2.711 |
r_mcbond_it | 2.037 |
r_angle_refined_deg | 1.684 |
r_angle_other_deg | 0.978 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11443 |
Nucleic Acid Atoms | |
Solvent Atoms | 1759 |
Heterogen Atoms | 73 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
SHELX | phasing |
MolProbity | model building |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
MOSFLM | data reduction |
SHELXD | phasing |
autoSHARP | phasing |