4QDR
Physical basis for Nrp2 ligand binding
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2QQJ | pdb entry 2QQJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | 0.1 M HEPES, 18% (w/v) PEG 12000, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.07 | 40.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 34.901 | α = 90 |
b = 70.759 | β = 90 |
c = 122.974 | 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 | 110 | CCD | MARMOSAIC 225 mm CCD | 2011-06-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-BM | 1.0000 | APS | 22-BM |
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 | 2.4 | 20 | 96.4 | 0.08 | 29.4 | 12715 | 12223 | -3 |
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 | 2.4 | 2.49 | 83.2 | 0.292 | 5.1 |
Refinement
Statistics | |||||||||||||||||||
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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 | pdb entry 2QQJ | 2.4 | 19.69 | 11490 | 586 | 96.26 | 0.20357 | 0.20089 | 0.25512 | RANDOM | 46.599 |
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] | |
-0.34 | 0.09 | 0.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.183 |
r_dihedral_angle_4_deg | 17.942 |
r_dihedral_angle_3_deg | 14.163 |
r_dihedral_angle_1_deg | 6.996 |
r_angle_refined_deg | 1.19 |
r_chiral_restr | 0.08 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.004 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2513 |
Nucleic Acid Atoms | |
Solvent Atoms | 123 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |