X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 293.0
Details 0.160 mM HcA2 (8.27 mg/mL), 0.160 mM SV2CL4 (2.24 mg/mL), 2 mM Sialylated Thomsen-Friedenreich carbohydrate antigen (Sialyl-T). Reservoir solution: 200 mM CaCl2, 100 mM MES pH 6.0, 20 % PEG 6000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.71 α = 90
b = 122.11 β = 90
c = 47.66 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2015-07-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.919908 BESSY 14.1

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
2 47.66 99.8 0.242 -- -- 13.2 -- 40692 -- -- --
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)
2.0 2.05 97.7 1.237 -- 2.2 13.4 --

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 2.0 47.66 -- -- -- 38627 2010 99.81 -- 0.18387 0.18139 0.22967 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 1.998 2.05 -- 114 2776 0.29 0.296 -- 97.6
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.539
Anisotropic B[1][1] 1.86
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.7
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.16
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_other 0.979
r_angle_other_deg 0.96
r_gen_planes_other 0.001
r_bond_other_d 0.002
r_long_range_B_refined 4.758
r_mcbond_it 0.962
r_chiral_restr 0.1
r_bond_refined_d 0.015
r_dihedral_angle_3_deg 14.658
r_dihedral_angle_4_deg 14.271
r_scbond_it 0.979
r_mcbond_other 0.959
r_dihedral_angle_1_deg 6.947
r_mcangle_other 1.665
r_dihedral_angle_2_deg 36.602
r_gen_planes_refined 0.007
r_scangle_other 1.633
r_long_range_B_other 4.758
r_mcangle_it 1.666
r_angle_refined_deg 1.663
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4234
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 359

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0158
XDS data reduction
Aimless data scaling
PHASER phasing