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Crystal structure of haspin in complex with 5-iodotubercidin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 51-63% MPD and 0.1M SPG buffer, pH 6.0-6.5
Crystal Properties Matthews coefficient Solvent content 3.03 59.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.58 α = 90 b = 78.74 β = 90 c = 79.73 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 PILATUS3 6M 2014-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9794 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.76 23.98 98.1 0.087 0.994 13.9 6.2 48665
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.79 96.8 0.224 0.968 7.2 6.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4OUC 1.76 23.98 46249 2373 97.75 0.14012 0.13833 0.17374 0.2025 RANDOM 21.753
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] 0.21 -0.68 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.903 r_dihedral_angle_4_deg 17.734 r_dihedral_angle_3_deg 12.002 r_sphericity_free 8.303 r_sphericity_bonded 6.771 r_dihedral_angle_1_deg 6.433 r_rigid_bond_restr 5.783 r_long_range_B_other 2.504 r_long_range_B_refined 2.501 r_scangle_other 2.369
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.903 r_dihedral_angle_4_deg 17.734 r_dihedral_angle_3_deg 12.002 r_sphericity_free 8.303 r_sphericity_bonded 6.771 r_dihedral_angle_1_deg 6.433 r_rigid_bond_restr 5.783 r_long_range_B_other 2.504 r_long_range_B_refined 2.501 r_scangle_other 2.369 r_scbond_it 2.116 r_scbond_other 2.096 r_mcangle_it 1.872 r_mcangle_other 1.871 r_angle_refined_deg 1.75 r_mcbond_other 1.551 r_mcbond_it 1.547 r_angle_other_deg 1.022 r_chiral_restr 0.118 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2588 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing