2O31

Crystal structure of the second SH3 domain from ponsin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729215% v/v Tascinamine, 0.1M HEPES, 2% w/v PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.0238.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 24.661α = 90
b = 35.499β = 90
c = 71.079γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2005-06-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8125EMBL/DESY, HAMBURGX11

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
11.51499.60.06523.15.9107521070710.754
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)
1.491.521000.2297.85.8515

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT1W701.513.36101243111000.131950.131140.16182RANDOM14.822
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]
0.44-0.810.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.988
r_sphericity_free11.895
r_dihedral_angle_4_deg10.767
r_dihedral_angle_3_deg10.699
r_dihedral_angle_1_deg6.416
r_sphericity_bonded5.45
r_scangle_it4.794
r_scbond_it3.716
r_mcangle_it2.637
r_rigid_bond_restr2.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.988
r_sphericity_free11.895
r_dihedral_angle_4_deg10.767
r_dihedral_angle_3_deg10.699
r_dihedral_angle_1_deg6.416
r_sphericity_bonded5.45
r_scangle_it4.794
r_scbond_it3.716
r_mcangle_it2.637
r_rigid_bond_restr2.077
r_mcbond_it1.882
r_angle_refined_deg1.611
r_nbtor_refined0.32
r_nbd_refined0.219
r_symmetry_vdw_refined0.158
r_xyhbond_nbd_refined0.131
r_chiral_restr0.122
r_symmetry_hbond_refined0.116
r_bond_refined_d0.017
r_gen_planes_refined0.011
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms553
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms

Software

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