1TFV

CRYSTAL STRUCTURE OF A BUFFALO SIGNALING GLYCOPROTEIN (SPB-40) SECRETED DURING INVOLUTION


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LJY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS829816% ETHANOL, 25MM TRIS, pH 8.0, MICRODIALYSIS, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.764α = 90
b = 66.559β = 90
c = 107.137γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295IMAGE PLATEMARRESEARCH1999-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5417

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
12.92075.50.171118070
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)
12.92.950.3422.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1LJY2.92080703181000.239870.237470.28806RANDOM41.247
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]
-2.26-2.034.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg3.879
r_angle_refined_deg1.928
r_symmetry_hbond_refined0.45
r_nbd_refined0.304
r_symmetry_vdw_refined0.261
r_xyhbond_nbd_refined0.249
r_chiral_restr0.134
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg3.879
r_angle_refined_deg1.928
r_symmetry_hbond_refined0.45
r_nbd_refined0.304
r_symmetry_vdw_refined0.261
r_xyhbond_nbd_refined0.249
r_chiral_restr0.134
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
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 Atoms64
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing