2OWM
Motor domain of Neurospora crassa kinesin-3 (NcKin3)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1I5S | TRUNCATED MODEL DERIVED FROM ADP COMPLEX OF KIF1A (1I5S) |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 7.5 | 293 | 1.5ul protein solution (50mM phosphate buffer pH 7.5, 150mM sodium chloride, 50uM ATP, 1mM magnesium chloride, EGTA, DTT) mixed with 0.5ul reservoir (0.1M Hepes pH 7.5, 0.2M sodium potassium tartrate, 24% PEG3350) and 0.2ul 0.1M magnesium chloride , VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 75.945 | α = 90 |
b = 98.408 | β = 91.86 |
c = 111.764 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | MAR CCD 165 mm | 2004-05-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | EMBL/DESY, HAMBURG | X13 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3.25 | 111.8 | 100 | 0.143 | 6 | 3.8 | 26100 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3.25 | 3.31 | 100 | 0.705 | 3.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | THROUGHOUT | TRUNCATED MODEL DERIVED FROM ADP COMPLEX OF KIF1A (1I5S) | 3.25 | 111.8 | 26084 | 24755 | 1329 | 100 | 0.213 | 0.21 | 0.256 | RANDOM | 74.79 |
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] | |
1.87 | 5.06 | 0.85 | -2.4 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.618 |
r_dihedral_angle_3_deg | 22.912 |
r_dihedral_angle_4_deg | 19.541 |
r_dihedral_angle_1_deg | 7.38 |
r_scangle_it | 1.867 |
r_angle_refined_deg | 1.844 |
r_scbond_it | 1.122 |
r_mcangle_it | 0.669 |
r_symmetry_hbond_refined | 0.425 |
r_mcbond_it | 0.386 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10226 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 112 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |