4GKP
Structure of the truncated neck and C-terminal motor homology domain of ViK1 from Candida glabrata
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2O0A | PDB entry 2O0A |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 277 | 0.1M HEPES, 13% PEG-6000, 5% isopropanol, 75mM NaAcetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.83 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.742 | α = 90 |
b = 77.722 | β = 90 |
c = 107.737 | 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 | ADSC QUANTUM 270 | 2008-10-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X6A | 0.976 | NSLS | X6A |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.42 | 20 | 98.8 | 0.035 | 37.65 | 7.8 | 22019 | 21752 | -3 | 49.904 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.42 | 2.5 | 92.7 | 0.193 | 8.17 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 2O0A | 2.42 | 19.83 | 22019 | 21751 | 1088 | 98.79 | 0.212 | 0.212 | 0.2095 | 0.2593 | RANDOM | 43.2617 |
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] | |
0.36 | -1.25 | 0.89 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.254 |
r_dihedral_angle_3_deg | 16.053 |
r_dihedral_angle_4_deg | 15.827 |
r_dihedral_angle_1_deg | 6.261 |
r_angle_refined_deg | 1.255 |
r_chiral_restr | 0.083 |
r_bond_refined_d | 0.009 |
r_gen_planes_refined | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3724 |
Nucleic Acid Atoms | |
Solvent Atoms | 80 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Blu-Ice | data collection |
XDS | data reduction |
PHASER | phasing |