X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details 2UL BUFFER (0.1 M SODIUM CACODYLATE PH 6.5, 0.2M MAGNESIUM ACETATE TETRAHYDRATE, 20% PEG 8000) PLUS 2UL OF LECTIN PROTEIN AT 10 MG/ML AND L-FUCOSE AT 137 UG/ML

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.97 α = 90
b = 86.41 β = 90.62
c = 77.85 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD MULTILAYER 2003-01-15
Diffraction Radiation
Monochromator Protocol
DIAMOND SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 -- ESRF ID14-1

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
1.5 19.96 96.8 0.049 -- -- 3.6 -- 534572 -- -- 14.4
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)
1.5 1.55 96.8 0.374 -- 18.4 2.8 --

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
OTHER 1.5 19.96 -- -- -- 92216 1884 96.8 -- -- 0.144 0.179 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 1.5 1.54 -- 107 5241 0.262 0.279 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.8
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 0.858
r_symmetry_hbond_refined 0.185
r_scbond_it 1.954
r_gen_planes_other 0.002
r_xyhbond_nbd_refined 0.18
r_dihedral_angle_1_deg 7.096
r_bond_refined_d 0.014
r_bond_other_d 0.016
r_nbd_other 0.277
r_scangle_it 2.956
r_symmetry_vdw_other 0.289
r_gen_planes_refined 0.008
r_mcangle_it 1.448
r_angle_other_deg 1.439
r_angle_refined_deg 1.54
r_nbtor_other 0.093
r_chiral_restr 0.099
r_nbd_refined 0.195
r_symmetry_vdw_refined 0.155
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4742
Nucleic Acid Atoms 0
Heterogen Atoms 132
Solvent Atoms 1166

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.19
MOSFLM data reduction
SCALA data scaling
autoSHARP phasing