2X7G

Structure of human serine-arginine-rich protein-specific kinase 2 (SRPK2) bound to purvalanol B


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WBPPDB ENTRY 1WBP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.750.5M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE PH4.75
Crystal Properties
Matthews coefficientSolvent content
3.665.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.31α = 90
b = 110.31β = 90
c = 90.59γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX2009-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I24DiamondI24

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
12.545.2199.70.136.53.22230643.1
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)
12.52.6499.60.5923.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1WBP2.54521171113599.460.186150.182920.180.248680.24RANDOM16.352
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]
0.080.040.08-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.143
r_dihedral_angle_4_deg16.742
r_dihedral_angle_3_deg14.205
r_scangle_it9.999
r_scbond_it7.692
r_dihedral_angle_1_deg5.792
r_mcangle_it4.091
r_mcbond_it2.452
r_angle_refined_deg1.368
r_angle_other_deg0.865
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2765
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms93

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing