4FS0
Crystal structure of mutant F136D of mouse nectin-2 extracellular fragment D1-D2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 4FMK | PDB ENTRY 4FMK |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293.15 | 1 M lithium sulfate, 0.6 M ammonium sulfate, 0.1 M tri-sodium citrate, pH 5.5, cryoprotectant: 30% w/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.18 | 43.63 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 59.857 | α = 90 |
b = 59.857 | β = 90 |
c = 210.013 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 65 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2012-03-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4C | 0.9792 | NSLS | X4C |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3.25 | 30 | 99.8 | 0.11 | 13.7 | 6.3 | 19387 | 19387 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 3.25 | 3.37 | 93.2 | 0.35 | 2.5 | 5.7 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4FMK | 3.25 | 20 | 19387 | 3532 | 375 | 98.76 | 0.24979 | 0.24979 | 0.24033 | 0.33476 | RANDOM | 52.836 |
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] | |
1.78 | 0.89 | 1.78 | -2.68 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.52 |
r_dihedral_angle_3_deg | 23.063 |
r_dihedral_angle_4_deg | 22.082 |
r_dihedral_angle_1_deg | 6.827 |
r_angle_refined_deg | 1.556 |
r_angle_other_deg | 1.13 |
r_chiral_restr | 0.077 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1684 |
Nucleic Acid Atoms | |
Solvent Atoms | 12 |
Heterogen Atoms | 43 |
Software
Software | |
---|---|
Software Name | Purpose |
ADSC | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |