4MTV

Crystal structure of the complex of Buffalo Signalling Glycoprotein with pentasaccharide at 2.8A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O9O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829825mM Tris, 50mM NaCl, 20% ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7355.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.87α = 90
b = 66.499β = 90
c = 107.126γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDMARRESEARCHoptics2007-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.856.592.40.1434.52362310772
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.995.80.3241.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2o9o2.856.5107221018150892.410.18370.18370.181420.22902RANDOM31.5201
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.5-0.40.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.792
r_dihedral_angle_4_deg25.785
r_dihedral_angle_3_deg21.694
r_dihedral_angle_1_deg5.942
r_angle_refined_deg2.509
r_chiral_restr0.198
r_gen_planes_refined0.017
r_bond_refined_d0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2893
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms85

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
AUTOMARdata reduction
SCALEPACKdata scaling