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Crystal structure of haspin in complex with 5-fluorotubercidin
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 59.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.711 α = 90 b = 78.89 β = 90 c = 79.63 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 2015-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 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 1.48 23.8 100 0.149 0.994 9.9 9.3 83206
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 1.48 1.51 100 0.648 2.5 5.5
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 MOLECULAR REPLACEMENT THROUGHOUT 4OUC 1.48 23.8 79010 4122 99.9 0.14916 0.14823 0.1472 0.16741 0.1673 RANDOM 19.777
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 -1.05 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.393 r_dihedral_angle_4_deg 18.891 r_dihedral_angle_3_deg 11.975 r_dihedral_angle_1_deg 6.368 r_sphericity_bonded 5.765 r_rigid_bond_restr 5.567 r_long_range_B_refined 2.163 r_long_range_B_other 2.163 r_scangle_other 1.947 r_scbond_it 1.666
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.393 r_dihedral_angle_4_deg 18.891 r_dihedral_angle_3_deg 11.975 r_dihedral_angle_1_deg 6.368 r_sphericity_bonded 5.765 r_rigid_bond_restr 5.567 r_long_range_B_refined 2.163 r_long_range_B_other 2.163 r_scangle_other 1.947 r_scbond_it 1.666 r_scbond_other 1.665 r_angle_refined_deg 1.605 r_mcangle_it 1.348 r_mcangle_other 1.348 r_mcbond_it 1.122 r_mcbond_other 1.121 r_angle_other_deg 0.978 r_chiral_restr 0.107 r_bond_refined_d 0.013 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 r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2590 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing