1YNK

Identification of Key residues of the NC6.8 Fab antibody fragment binding to synthetic sweeteners: Crystal structure of NC6.8 co-crystalized with high potency sweetener compound SC45647


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 9.2
Temperature 291.0
Details 50 mM potassium hydrogen phosphate, 20% polyethylene glycol, pH 9.2, EVAPORATION, temperature 18C, pH 9.20, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 135.6 α = 90
b = 48.19 β = 109.04
c = 75.35 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1999-09-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID -- APS 19-ID

Data Collection

Overall
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
2.1 23.64 -- 0.3217 -- -- -- -- 24844 -- 2.85 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.1 -- -- -- -- 2.9 -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.1 23.64 -- -- -- 23597 1246 92.7 -- 0.216 0.213 0.277 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.1 2.15 -- 69 1152 0.272 0.367 -- 62.33
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.62
Anisotropic B[1][1] 1.22
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.79
Anisotropic B[2][2] -2.75
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.01
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.251
r_scbond_it 1.677
r_mcbond_it 0.862
r_dihedral_angle_4_deg 23.42
r_symmetry_vdw_refined 0.249
r_chiral_restr 0.155
r_angle_refined_deg 2.459
r_scangle_it 2.408
r_gen_planes_refined 0.012
r_mcangle_it 1.479
r_dihedral_angle_2_deg 34.054
r_nbtor_refined 0.325
r_symmetry_hbond_refined 0.24
r_dihedral_angle_3_deg 18.156
r_xyhbond_nbd_refined 0.177
r_bond_refined_d 0.027
r_dihedral_angle_1_deg 8.681
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3345
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 126

Software

Software
Software Name Purpose
HKL-2000 data collection
SCALEPACK data scaling
shake model building version: & Warp
REFMAC refinement version: 5.1
HKL-2000 data reduction
SnB phasing
ARP/wARP model building