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Crystal structure of human SRPK1 complexed to an inhibitor SRPIN340
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WAK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.1M sodium citrate, 0.2M ammonium acetate, 5%PEG6000
Crystal Properties Matthews coefficient Solvent content 2.77 55.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.132 α = 90 b = 75.132 β = 90 c = 310.623 γ = 120
Symmetry Space Group P 65 2 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 CCD ADSC QUANTUM 315 2014-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 50 99.5 0.056 71.03 20.9 36614
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 99 21.5
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 THROUGHOUT 1WAK 2 49.87 34331 1840 99.54 0.19861 0.19661 0.2077 0.23634 0.2417 RANDOM 36.412
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] 0.5 0.25 0.5 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.489 r_dihedral_angle_4_deg 20.706 r_dihedral_angle_3_deg 14.875 r_long_range_B_refined 7.587 r_long_range_B_other 7.578 r_scangle_other 6.128 r_dihedral_angle_1_deg 5.849 r_scbond_it 4.134 r_scbond_other 4.129 r_mcangle_it 4.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.489 r_dihedral_angle_4_deg 20.706 r_dihedral_angle_3_deg 14.875 r_long_range_B_refined 7.587 r_long_range_B_other 7.578 r_scangle_other 6.128 r_dihedral_angle_1_deg 5.849 r_scbond_it 4.134 r_scbond_other 4.129 r_mcangle_it 4.077 r_mcangle_other 4.076 r_mcbond_it 3.155 r_mcbond_other 3.155 r_angle_refined_deg 1.848 r_angle_other_deg 0.872 r_chiral_restr 0.117 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 2791 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing SCALEPACK data scaling PHASER phasing