3HN4
Crystal structure of the NK2 fragment (28-289) of human hepatocyte growth factor/scatter factor
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 298 | 50 mM Ammonium sulfate, 17-23% PEG 2000 or 4000, 100 mM HEPES pH 8.0, 5% 2-Methyl-2,4-pentanediol, 0.5 mM Beta-octyl glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.13 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.15 | α = 90 |
b = 48.15 | β = 90 |
c = 461.673 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 2 |
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 | MARMOSAIC 300 mm CCD | 2008-12-17 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | 2008-12-17 | M | SINGLE WAVELENGTH | ||||||
3 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | 2009-03-05 | M | SINGLE WAVELENGTH | ||||||
4 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | 2009-03-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.12700 | APS | 21-ID-D |
2 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.12700 | APS | 21-ID-D |
3 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97860 | APS | 21-ID-G |
4 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.07800 | APS | 21-ID-D |
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 | |||||||
1,2,3,4 | 2.4 | 50 | 93.7 | 0.134 | 0.134 | 9.3 | 6.4 | 13803 | 13803 |
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) | ||||||||||
2.4 | 2.44 | 74.3 | 0.447 | 0.447 | 1.1 | 2.8 |
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 | THROUGHOUT | PDB entry 1NK1 | 2.6 | 41.52 | 13740 | 10223 | 1028 | 100 | 0.26952 | 0.26268 | 0.33296 | RANDOM | 37.752 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.18 | 0.09 | 0.18 | -0.27 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.406 |
r_dihedral_angle_3_deg | 15.433 |
r_dihedral_angle_4_deg | 13.82 |
r_dihedral_angle_1_deg | 4.58 |
r_angle_refined_deg | 0.867 |
r_scangle_it | 0.542 |
r_mcangle_it | 0.367 |
r_scbond_it | 0.301 |
r_mcbond_it | 0.199 |
r_chiral_restr | 0.059 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2089 |
Nucleic Acid Atoms | |
Solvent Atoms | 106 |
Heterogen Atoms | 41 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CNS | refinement |
HKL-2000 | data reduction |
MOSFLM | data reduction |
HKL-2000 | data scaling |
SCALA | data scaling |
PHASER | phasing |