1SSH

Crystal structure of the SH3 domain from a S. cerevisiae hypothetical 40.4 kDa protein in complex with a peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72952.9M sodium malonate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0840.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.92α = 90
b = 33.92β = 90
c = 113.1γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7A0.9795EMBL/DESY, HAMBURGBW7A

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
11.42099.90.10116.567.413804-319.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.5100

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 REPLACEMENTTHROUGHOUT1OOT1.418.821311369199.890.16520.163260.2025RANDOM6.76
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]
-0.6-0.61.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.772
r_scangle_it3.652
r_scbond_it2.355
r_mcangle_it2.003
r_angle_refined_deg1.558
r_mcbond_it1.33
r_angle_other_deg0.831
r_symmetry_vdw_other0.308
r_nbd_other0.251
r_symmetry_hbond_refined0.202
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.772
r_scangle_it3.652
r_scbond_it2.355
r_mcangle_it2.003
r_angle_refined_deg1.558
r_mcbond_it1.33
r_angle_other_deg0.831
r_symmetry_vdw_other0.308
r_nbd_other0.251
r_symmetry_hbond_refined0.202
r_nbd_refined0.201
r_xyhbond_nbd_refined0.199
r_chiral_restr0.1
r_nbtor_other0.086
r_symmetry_vdw_refined0.071
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms556
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
AMoREphasing