4MPK

Crystal structure of the complex of buffalo signaling protein SPB-40 with N-acetylglucosamine at 2.65 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1829825mM Tris, 50mM NaCl, 20% ethanol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6753.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.938α = 90
b = 67.11β = 90
c = 107.006γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMIRROR2013-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
12.65501000.10217.813282
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)
12.652.71000.4334.5

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2O9O2.6541.61132821260465599.80.1770.1740.234RANDOM25.78
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]
-0.47-1.091.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.41
r_dihedral_angle_4_deg23.86
r_dihedral_angle_3_deg21.446
r_long_range_B_refined7.256
r_long_range_B_other7.232
r_dihedral_angle_1_deg6.998
r_scangle_other4.318
r_mcangle_other3.672
r_mcangle_it3.665
r_scbond_it2.557
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.41
r_dihedral_angle_4_deg23.86
r_dihedral_angle_3_deg21.446
r_long_range_B_refined7.256
r_long_range_B_other7.232
r_dihedral_angle_1_deg6.998
r_scangle_other4.318
r_mcangle_other3.672
r_mcangle_it3.665
r_scbond_it2.557
r_scbond_other2.556
r_mcbond_it2.131
r_mcbond_other2.095
r_angle_refined_deg1.807
r_angle_other_deg0.947
r_chiral_restr0.097
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2894
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms35

Software

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