3CA7

High Resolution Crystal Structure of the EGF domain of Spitz


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.529415mM ammonium sulphate, 0.1M MES pH 6.5, 24% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.1743.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.305α = 90
b = 36.154β = 103.09
c = 25.362γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD3.0 UNDULATOR2007-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.4995091.60.04716.35.37284-320.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.4991.5556.60.214.63.6

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1JL91.530.57634728435091.50.2010.20.236RANDOM20.66
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]
-0.45-0.920.96-0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.263
r_dihedral_angle_3_deg13.785
r_dihedral_angle_4_deg11.741
r_dihedral_angle_1_deg6.683
r_scangle_it3.222
r_scbond_it2.152
r_mcangle_it1.535
r_angle_refined_deg1.165
r_mcbond_it1.083
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.263
r_dihedral_angle_3_deg13.785
r_dihedral_angle_4_deg11.741
r_dihedral_angle_1_deg6.683
r_scangle_it3.222
r_scbond_it2.152
r_mcangle_it1.535
r_angle_refined_deg1.165
r_mcbond_it1.083
r_nbtor_refined0.313
r_nbd_refined0.199
r_symmetry_hbond_refined0.169
r_symmetry_vdw_refined0.162
r_xyhbond_nbd_refined0.115
r_chiral_restr0.082
r_bond_refined_d0.009
r_gen_planes_refined0.005
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 Atoms406
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms

Software

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