1WBP

SRPK1 bound to 9mer docking motif peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WAKPDB ENTRY 1WAK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17100MM SODIUM CITRATE PH5.6, 200MM AMMONIUM ACETATE, 15%PEG3350, 5MM PEPTIDE, 5MM ADP, 10MM MGCL2, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
2.9958.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.68α = 90
b = 78.68β = 90
c = 310.54γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray105CCDADSC CCD2003-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

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
12.43097.80.078.11122765110.9
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)
12.42.49840.562.97.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1WAK2.428.2621561347667.10.2280.2280.247RANDOM96.2
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]
21.314.5921.3-42.61
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.2
c_mcangle_it11.44
c_scangle_it10.7
c_mcbond_it8.48
c_scbond_it8.26
c_angle_deg1.4
c_improper_angle_d0.74
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.2
c_mcangle_it11.44
c_scangle_it10.7
c_mcbond_it8.48
c_scbond_it8.26
c_angle_deg1.4
c_improper_angle_d0.74
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2910
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms31

Software

Software
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing