4KZN
crystal structure of human VEGF-A receptor binding domain
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1VPF | pdb 1vpf |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 295 | Li2SO4, PEG200, Tris buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 54.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 87.573 | α = 90 |
b = 32.014 | β = 92.99 |
c = 42.981 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | ADSC QUANTUM 315 | monochromator | 2009-02-04 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | mirror | 2008-12-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSRRC BEAMLINE BL13B1 | 1.0 | NSRRC | BL13B1 |
2 | SYNCHROTRON | NSRRC BEAMLINE BL13C1 | 1.0 | NSRRC | BL13C1 |
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 | 1.71 | 30 | 97.4 | 0.045 | 17.7 | 3.5 | 12694 | 19.7817489644 |
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 | 1.71 | 1.77 | 96.4 | 0.271 | 3.2 | 1223 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 1vpf | 1.7114 | 24.8338014786 | 1.38318867874 | 12685 | 12685 | 1275 | 97.0691766146 | 0.182783276428 | 0.178919069691 | 0.218229685236 | random | 5.51618585435 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 32.619799158 |
f_angle_d | 1.55912244699 |
f_chiral_restr | 0.0983048194363 |
f_bond_d | 0.0117018840049 |
f_plane_restr | 0.00608210773817 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 770 |
Nucleic Acid Atoms | |
Solvent Atoms | 63 |
Heterogen Atoms | 86 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
RESOLVE | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |