3FIL
Structural and energetic determinants for hyperstable variants of GB1 obtained from in-vitro evolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1PGA | PDB ENTRY 1PGA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 293.15 | protein solution: 50mM sodium acetate pH 5.6, 50mg/ml protein. reservoir solution: 25% PEG 3350, 0.1M citric acids pH 3.5. Drop 400nl protein solution & 400nl reservoir solution, 80 micro-l reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.93 | 39.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 29.694 | α = 90 |
b = 38.93 | β = 90 |
c = 83.326 | 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 | 110 | CCD | RAYONIX MX-225 | Mirror 1: Silicon, active surface 50nm Rh-coated. Mirror 2: Glas, active surface 50 nm Rh-coated. | 2006-03-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 0.88561 | BESSY | 14.2 |
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 | 0.842 | 19.466 | 97.3 | 0.074 | 0.063 | 13.26 | 7.08 | 87156 | 86548 | 11.564 |
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) | ||||||||||
0.84 | 0.98 | 84.8 | 0.481 | 0.775 | 2.56 | 5.82 | 9687 |
Refinement
Statistics | |||||||||||||||||||
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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 | FREE R | PDB ENTRY 1PGA | 0.88 | 19.466 | 77514 | 76999 | 99.3 | 0.125 | 0.1239 | 0.1493 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
17 | 853 | 1102.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_non_zero_chiral_vol | 0.086 |
s_approx_iso_adps | 0.083 |
s_zero_chiral_vol | 0.075 |
s_anti_bump_dis_restr | 0.071 |
s_similar_adp_cmpnt | 0.037 |
s_from_restr_planes | 0.0302 |
s_angle_d | 0.027 |
s_bond_d | 0.013 |
s_rigid_bond_adp_cmpnt | 0.006 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 939 |
Nucleic Acid Atoms | |
Solvent Atoms | 245 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
AMoRE | phasing |
SHELXL-97 | refinement |
XDS | data reduction |
XSCALE | data scaling |