4MBZ | pdb_00004mbz

Structure of B-Lymphotropic Polyomavirus VP1 in complex with 3'-sialyllactosamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherLPyV Native structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.829312% (v/v) Isopropanol, 0.2 M calcium chloride, 0.1 M sodium acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8256.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.16α = 90
b = 97.24β = 96.21
c = 234.22γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93PIXELDECTRIS PILATUS 2M-F2012-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.755099.114.63.1336648333435-3-327.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.898.12.33.124809

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTLPyV Native structure1.7548.753366473167381669699.040.166250.166250.164730.160.194850.2RANDOM26.229
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]
-0.21-0.120.45-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.621
r_dihedral_angle_4_deg19.656
r_dihedral_angle_3_deg11.977
r_long_range_B_refined7.583
r_dihedral_angle_1_deg5.818
r_scbond_it2.43
r_mcangle_it2.035
r_mcbond_it1.314
r_angle_refined_deg1.299
r_chiral_restr0.086
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20872
Nucleic Acid Atoms
Solvent Atoms2900
Heterogen Atoms390

Software

Software
Software NamePurpose
RemDAqdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling