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Crystal structure of human Haspin (GSG2) kinase bound to chemical probe MU1920
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Z59
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 278 45% MPD
0.1M SPG 6.5
Crystal Properties Matthews coefficient Solvent content 3.16 61.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.558 α = 90 b = 75.891 β = 90 c = 84.16 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2022-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999990 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.4 45.22 99.9 0.998 12 3.4 19530
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 0.768
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.4 45.22 18501 982 99.86 0.18669 0.18392 0.1983 0.23881 0.2502 RANDOM 54.563
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] 0.99 2.07 -3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.217 r_dihedral_angle_2_deg 9.546 r_long_range_B_other 8.46 r_long_range_B_refined 8.453 r_dihedral_angle_1_deg 7.261 r_scangle_other 6.653 r_mcangle_it 4.773 r_mcangle_other 4.773 r_scbond_it 4.298 r_scbond_other 4.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.217 r_dihedral_angle_2_deg 9.546 r_long_range_B_other 8.46 r_long_range_B_refined 8.453 r_dihedral_angle_1_deg 7.261 r_scangle_other 6.653 r_mcangle_it 4.773 r_mcangle_other 4.773 r_scbond_it 4.298 r_scbond_other 4.296 r_mcbond_it 3.198 r_mcbond_other 3.197 r_angle_refined_deg 1.469 r_angle_other_deg 0.485 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2553 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing