1XHG

Crystal structure of a 40 kDa signalling protein from Porcine (SPP-40) at 2.89A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.829825mM tris-HCl, 50mM NaCl, 20% ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.856.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.75α = 90
b = 66.454β = 90
c = 107.652γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMARRESEARCHMIRROR2004-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5412

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
12.895690.70.133.37.310510947636.7
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)
12.89387.10.5421.3

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 REPLACEMENTTHROUGHOUTPDB entry 1OWQ2.9569476902645090.220.180.179110.177230.21765RANDOM28.47
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]
-0.91-0.971.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg21.681
r_scangle_it5.032
r_dihedral_angle_1_deg3.142
r_scbond_it3.058
r_mcangle_it2.528
r_angle_refined_deg2.015
r_angle_other_deg1.486
r_mcbond_it1.355
r_symmetry_vdw_other0.461
r_nbtor_other0.393
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg21.681
r_scangle_it5.032
r_dihedral_angle_1_deg3.142
r_scbond_it3.058
r_mcangle_it2.528
r_angle_refined_deg2.015
r_angle_other_deg1.486
r_mcbond_it1.355
r_symmetry_vdw_other0.461
r_nbtor_other0.393
r_symmetry_vdw_refined0.356
r_nbd_refined0.281
r_nbd_other0.259
r_symmetry_hbond_refined0.228
r_xyhbond_nbd_refined0.164
r_chiral_restr0.117
r_xyhbond_nbd_other0.086
r_bond_refined_d0.023
r_gen_planes_refined0.007
r_gen_planes_other0.005
r_bond_other_d0.003
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2875
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing