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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1WBP2.54521171113599.460.186150.182920.24868RANDOM16.352
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
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
r_mcbond_other0.627
r_symmetry_vdw_other0.262
r_nbd_refined0.214
r_nbtor_refined0.184
r_symmetry_hbond_refined0.178
r_nbd_other0.176
r_xyhbond_nbd_refined0.137
r_symmetry_vdw_refined0.099
r_nbtor_other0.085
r_chiral_restr0.076
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
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