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Crystal structure of haspin in complex with tubercidin
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 3.04 59.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.56 α = 90 b = 78.76 β = 90 c = 80.02 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 1.43 24.05 99.9 0.102 0.994 8.6 5.9 92144
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 1.43 1.45 98.3 0.379 1.2 4.2
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 4OUC 1.47 24.05 80839 4169 99.96 0.14437 0.14326 0.1429 0.16544 0.1644 RANDOM 22.281
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] -0.58 0.03 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.711 r_dihedral_angle_4_deg 16.086 r_dihedral_angle_3_deg 10.957 r_sphericity_bonded 10.882 r_dihedral_angle_1_deg 6.391 r_rigid_bond_restr 3.679 r_long_range_B_refined 3.024 r_long_range_B_other 3.024 r_scangle_other 2.902 r_scbond_it 2.601
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.711 r_dihedral_angle_4_deg 16.086 r_dihedral_angle_3_deg 10.957 r_sphericity_bonded 10.882 r_dihedral_angle_1_deg 6.391 r_rigid_bond_restr 3.679 r_long_range_B_refined 3.024 r_long_range_B_other 3.024 r_scangle_other 2.902 r_scbond_it 2.601 r_scbond_other 2.51 r_mcangle_it 1.949 r_mcangle_other 1.949 r_mcbond_it 1.671 r_mcbond_other 1.583 r_angle_refined_deg 1.537 r_angle_other_deg 0.967 r_chiral_restr 0.1 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_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2579 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing