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 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_scangle_it 2.956
r_scbond_it 1.954
r_mcangle_it 1.448
r_mcbond_it 0.858
r_nbd_refined 0.195
r_gen_planes_other 0.002
r_gen_planes_refined 0.008
r_chiral_restr 0.099
r_dihedral_angle_1_deg 7.096
r_angle_other_deg 1.439
r_angle_refined_deg 1.54
r_bond_other_d 0.016
r_bond_refined_d 0.014
r_nbd_other 0.277
r_nbtor_other 0.093
r_xyhbond_nbd_refined 0.18
r_symmetry_vdw_refined 0.155
r_symmetry_vdw_other 0.289
r_symmetry_hbond_refined 0.185
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

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AUTOSHARP Structure Solution
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.19 refinement
AUTOSHARP model building