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Cocomplex structure of Deoxyhypusine synthase with inhibitor 6-[(2R)-1-AMINO-4-METHYLPENTAN-2-YL]-3-(PYRIDIN-3-YL)-4H,5H,6H,7H-THIENO[2,3-C]PYRIDIN-7-ONE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6P4V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 100mM Hepes, 2.0M Na/K Phosphate
Crystal Properties Matthews coefficient Solvent content 3.09 60.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.988 α = 90 b = 105.988 β = 90 c = 157.068 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210 2013-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.078 NSLS X6A
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 2.12 50 95.4 0.135 15.55 3.7 58565
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.16 0.94
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 6P4V 2.12 43.97 53246 2845 99.94 0.17953 0.17872 0.188 0.1944 0.2036 RANDOM 34.141
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] 1.3 0.65 1.3 -1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.525 r_dihedral_angle_4_deg 20.883 r_dihedral_angle_3_deg 13.053 r_dihedral_angle_1_deg 5.499 r_angle_refined_deg 1.212 r_angle_other_deg 0.748 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.525 r_dihedral_angle_4_deg 20.883 r_dihedral_angle_3_deg 13.053 r_dihedral_angle_1_deg 5.499 r_angle_refined_deg 1.212 r_angle_other_deg 0.748 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4528 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing