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The crystal structure of KanD2 in complex with NADH and 3"-deamino-3"-hydroxykanamycin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H3V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 8000, imidazole, calcium acetate, NADH, 3"-deamino-3"-hydroxykanamycin A
Crystal Properties Matthews coefficient Solvent content 3.33 63.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.01 α = 90 b = 120.01 β = 90 c = 132.86 γ = 120
Symmetry Space Group P 31 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 100 CCD ADSC QUANTUM 315r 2018-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.36 50 100 0.111 15.8 11.1 45963
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.36 2.49 100 0.996 2.3 11.2
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 4H3V 2.36 44.57 43605 2319 99.96 0.2052 0.2038 0.2105 0.23125 0.2326 RANDOM 54.231
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] 0.78 0.78 0.78 -2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.385 r_dihedral_angle_4_deg 23.208 r_dihedral_angle_3_deg 18.107 r_dihedral_angle_1_deg 6.466 r_angle_refined_deg 2.073 r_angle_other_deg 1.214 r_chiral_restr 0.116 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.385 r_dihedral_angle_4_deg 23.208 r_dihedral_angle_3_deg 18.107 r_dihedral_angle_1_deg 6.466 r_angle_refined_deg 2.073 r_angle_other_deg 1.214 r_chiral_restr 0.116 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 5172 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing