1ZBC

Crystal Structure of the porcine signalling protein liganded with the peptide Trp-Pro-Trp (WPW) at 2.3 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.829925mM Tris-HCl, 14% ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 299K
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.35α = 90
b = 66.48β = 90
c = 107.026γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray290IMAGE PLATEMARRESEARCHMirror2004-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
12.356.899.30.11210192231922331.5
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)
12.32.3897.50.6822.1

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 REPLACEMENTTHROUGHOUT1XRV2.29201922319223103998.830.2040.198220.193240.23479RANDOM28.165
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]
-0.08-0.450.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg20.212
r_dihedral_angle_1_deg5.051
r_scangle_it4.144
r_scbond_it2.399
r_angle_refined_deg2.325
r_mcangle_it1.862
r_angle_other_deg1.541
r_mcbond_it0.958
r_symmetry_vdw_other0.561
r_symmetry_vdw_refined0.388
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg20.212
r_dihedral_angle_1_deg5.051
r_scangle_it4.144
r_scbond_it2.399
r_angle_refined_deg2.325
r_mcangle_it1.862
r_angle_other_deg1.541
r_mcbond_it0.958
r_symmetry_vdw_other0.561
r_symmetry_vdw_refined0.388
r_nbtor_other0.341
r_nbd_refined0.264
r_nbd_other0.245
r_symmetry_hbond_refined0.185
r_xyhbond_nbd_refined0.155
r_chiral_restr0.154
r_xyhbond_nbd_other0.144
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_gen_planes_other0.005
r_bond_other_d0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2910
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms28

Software

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