3PYC

Crystal structure of human SMURF1 C2 domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1M HEPES (pH 6.5), 2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2445.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.959α = 90
b = 47.048β = 90
c = 91.266γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.965099.6101541011322

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.9632.76958648599.610.205820.204130.24115RANDOM23.774
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]
2.51-1.12-1.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.207
r_dihedral_angle_3_deg17.531
r_dihedral_angle_4_deg13.537
r_dihedral_angle_1_deg6.807
r_scangle_it5.332
r_scbond_it3.352
r_mcangle_it2.054
r_angle_refined_deg1.7
r_mcbond_it1.25
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.207
r_dihedral_angle_3_deg17.531
r_dihedral_angle_4_deg13.537
r_dihedral_angle_1_deg6.807
r_scangle_it5.332
r_scbond_it3.352
r_mcangle_it2.054
r_angle_refined_deg1.7
r_mcbond_it1.25
r_nbtor_refined0.311
r_nbd_refined0.235
r_symmetry_vdw_refined0.213
r_symmetry_hbond_refined0.176
r_xyhbond_nbd_refined0.154
r_chiral_restr0.14
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms1038
Nucleic Acid Atoms
Solvent Atoms54
Heterogen Atoms11

Software

Software
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling