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Crystal structure of human SR protein kinase 1 (SRPK1) in complex with compound 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WAK 1wak, 1wbp experimental model PDB 1WBP 1wak, 1wbp
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277.15 0.1 M tris pH 7.5, 0.1 M CaCl2, 20% PEG6K, 11% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.51 51.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.572 α = 90 b = 82.572 β = 90 c = 133.837 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2014-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9795 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.75 29.29 99.8 0.059 0.023 28.4 14.2 47639 21.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 96 0.826 0.323 3.7 13.8
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 1wak, 1wbp 1.75 29.29 45207 2354 99.76 0.17479 0.1732 0.1835 0.20533 0.2159 RANDOM 29.591
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] -0.18 -0.18 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.311 r_dihedral_angle_4_deg 16.44 r_dihedral_angle_3_deg 12.691 r_long_range_B_refined 6.357 r_long_range_B_other 6.263 r_dihedral_angle_1_deg 5.976 r_scangle_other 4.665 r_scbond_it 2.927 r_scbond_other 2.927 r_mcangle_other 2.787
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.311 r_dihedral_angle_4_deg 16.44 r_dihedral_angle_3_deg 12.691 r_long_range_B_refined 6.357 r_long_range_B_other 6.263 r_dihedral_angle_1_deg 5.976 r_scangle_other 4.665 r_scbond_it 2.927 r_scbond_other 2.927 r_mcangle_other 2.787 r_mcangle_it 2.784 r_mcbond_it 1.913 r_mcbond_other 1.909 r_angle_refined_deg 1.546 r_angle_other_deg 0.951 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2932 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing