☰ Navigation Tabs
Structure of human serine-arginine-rich protein-specific kinase 2 (SRPK2) bound to purvalanol B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WBP PDB ENTRY 1WBP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.75 0.5M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE PH4.75
Crystal Properties Matthews coefficient Solvent content 3.6 65.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.31 α = 90 b = 110.31 β = 90 c = 90.59 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX 2009-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.5 45.21 99.7 0.13 6.5 3.2 22306 43.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 99.6 0.59 2 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1WBP 2.5 45 21171 1135 99.46 0.18615 0.18292 0.18 0.24868 0.2389 RANDOM 16.352
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] 0.08 0.04 0.08 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.143 r_dihedral_angle_4_deg 16.742 r_dihedral_angle_3_deg 14.205 r_scangle_it 9.999 r_scbond_it 7.692 r_dihedral_angle_1_deg 5.792 r_mcangle_it 4.091 r_mcbond_it 2.452 r_angle_refined_deg 1.368 r_angle_other_deg 0.865
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.143 r_dihedral_angle_4_deg 16.742 r_dihedral_angle_3_deg 14.205 r_scangle_it 9.999 r_scbond_it 7.692 r_dihedral_angle_1_deg 5.792 r_mcangle_it 4.091 r_mcbond_it 2.452 r_angle_refined_deg 1.368 r_angle_other_deg 0.865 r_mcbond_other 0.627 r_symmetry_vdw_other 0.262 r_nbd_refined 0.214 r_nbtor_refined 0.184 r_symmetry_hbond_refined 0.178 r_nbd_other 0.176 r_xyhbond_nbd_refined 0.137 r_symmetry_vdw_refined 0.099 r_nbtor_other 0.085 r_chiral_restr 0.076 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.001 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 Atoms Number Protein Atoms 2765 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing