1TJ6

Crystal structure of the Xenopus tropicalis Spred1 EVH-1 domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8291PEG 3350, potassium fluoride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9436.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.881α = 90
b = 38.267β = 95.58
c = 80.226γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVmirrors2004-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.542

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.652596.20.0520.05238.26.2241892327316.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.651.6994.60.2110.2119.355.71497

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 1EVH1.65252418923262118896.080.15390.15390.1510.181RANDOM13.099
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]
0.37-0.06-0.50.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.797
r_scangle_it4.035
r_scbond_it2.402
r_mcangle_it1.695
r_angle_refined_deg1.507
r_mcbond_it0.954
r_angle_other_deg0.856
r_symmetry_vdw_other0.347
r_nbd_other0.266
r_symmetry_vdw_refined0.208
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.797
r_scangle_it4.035
r_scbond_it2.402
r_mcangle_it1.695
r_angle_refined_deg1.507
r_mcbond_it0.954
r_angle_other_deg0.856
r_symmetry_vdw_other0.347
r_nbd_other0.266
r_symmetry_vdw_refined0.208
r_symmetry_hbond_refined0.204
r_nbd_refined0.202
r_xyhbond_nbd_refined0.183
r_nbtor_other0.128
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_gen_planes_other0.008
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
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 Atoms1706
Nucleic Acid Atoms
Solvent Atoms303
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing