2CYG

Crystal structure at 1.45- resolution of the major allergen endo-beta-1,3-glucanase of banana as a molecular basis for the latex-fruit syndrome



X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 293.0
Details Sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.27 α = 90
b = 53.93 β = 90
c = 113.55 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-12-04
Diffraction Radiation
Monochromator Protocol
single wavelength SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2

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
1.45 20 97.7 0.035 0.035 -- 3.6 53238 52014 0.0 0.0 10.46
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)
1.45 1.5 97.7 0.129 0.129 5.6 3.6 4819

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 1.45 20.0 0.0 0.0 52014 49317 2644 97.4 0.15835 0.15835 0.15722 0.1794 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 1.45 1.487 3416 194 3416 0.16 0.189 -- 0.05
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.92
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_other 0.188
r_chiral_restr 0.067
r_symmetry_vdw_refined 0.097
r_gen_planes_refined 0.004
r_nbd_other 0.229
r_angle_refined_deg 1.095
r_xyhbond_nbd_refined 0.118
r_symmetry_hbond_refined 0.124
r_mcbond_it 0.384
r_scbond_it 1.206
r_mcangle_it 0.761
r_scangle_it 1.938
r_bond_refined_d 0.006
r_nbd_refined 0.195
r_angle_other_deg 0.787
r_gen_planes_other 0.001
r_nbtor_other 0.078
r_dihedral_angle_1_deg 6.01
r_bond_other_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2395
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 407

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.19
DENZO data reduction
CCP4 data scaling version: (SCALA)
AMoRE phasing