5XX4
A BPTI-[5,55] variant with C14GA38K mutations
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2ZVX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293.15 | 30% PEG4000; 0.2M Lithium Sulfate; 0.1M Tris-HCL, pH8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 25.201 | α = 90 |
b = 41.171 | β = 100.44 |
c = 54.742 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 101.15 | CCD | AGILENT EOS CCD | 2010-11-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NE3A | 1.0 | Photon Factory | AR-NE3A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.67 | 53.84 | 99.4 | 4.23 | 3.6 | 12943 |
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 | 1.67 | 1.73 | 95.9 | 0.223 | 0.223 | 4.87 | 2.8 |
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 | 2ZVX | 1.67 | 53.84 | 12243 | 627 | 99.38 | 0.14566 | 0.14197 | 0.22039 | RANDOM | 14.34 |
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] | |
0.75 | 0.35 | -0.57 | -0.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 23.377 |
r_dihedral_angle_2_deg | 23.099 |
r_dihedral_angle_4_deg | 15.802 |
r_dihedral_angle_3_deg | 10.922 |
r_sphericity_bonded | 9.016 |
r_dihedral_angle_1_deg | 7.052 |
r_rigid_bond_restr | 5.781 |
r_long_range_B_refined | 4.36 |
r_long_range_B_other | 3.521 |
r_scbond_it | 2.572 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 887 |
Nucleic Acid Atoms | |
Solvent Atoms | 231 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
SHELXL | data collection |
DENZO | data reduction |
SCALA | data scaling |
REFMAC | refinement |