2QE8
Crystal structure of a putative hydrolase (ava_4197) from anabaena variabilis atcc 29413 at 1.35 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 10.5 | 277 | NANODROP, 0.8M K2HPO4, 0.2M Li2SO4, 1.2M NaH2PO4, 0.1M CAPS pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
2 | VAPOR DIFFUSION, SITTING DROP | 6 | 277 | NANODROP, 1.6M (NH4)2SO4, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 115.831 | α = 90 |
b = 135.562 | β = 90 |
c = 51.519 | γ = 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 | 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing | 2007-06-06 | M | SINGLE WAVELENGTH | |||||
2 | 2 | x-ray | 100 | CCD | MARMOSAIC 325 mm CCD | Flat collimating mirror, toroid focusing mirror | 2007-06-04 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL1-5 | 0.980910 | SSRL | BL1-5 |
2 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.97929, 0.89194, 0.97905 | SSRL | BL9-2 |
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 | |||||||
1,2 | 1.35 | 29.348 | 95.9 | 0.052 | 0.052 | 8.2 | 4.8 | 170743 | 13.57 |
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) | ||||||||||
1,2 | 1.35 | 1.39 | 73.9 | 0.346 | 0.346 | 1.1 | 2.1 | 9561 |
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 | 1.35 | 29.348 | 170682 | 8613 | 95.79 | 0.117 | 0.116 | 0.144 | RANDOM | 13.292 |
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] | |
0.28 | -0.75 | 0.47 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.588 |
r_dihedral_angle_4_deg | 11.679 |
r_dihedral_angle_3_deg | 11.322 |
r_sphericity_free | 10.036 |
r_dihedral_angle_1_deg | 6.868 |
r_scangle_it | 5.857 |
r_sphericity_bonded | 4.969 |
r_scbond_it | 4.604 |
r_mcangle_it | 3.711 |
r_mcbond_it | 2.836 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5178 |
Nucleic Acid Atoms | |
Solvent Atoms | 833 |
Heterogen Atoms | 124 |
Software
Software | |
---|---|
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 |
SHARP | phasing |