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Crystal structure of NE0047 (E143D) mutant in complex with 8-azaguanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HRQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.225M MgCl2, 25% PEG 3350, 0.1M Bis-Tris, PH 5.5
Crystal Properties Matthews coefficient Solvent content 1.91 35.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.491 α = 90 b = 73.629 β = 90 c = 109.997 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 CCD MARMOSAIC 225 mm CCD 2016-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.98 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.66 50 99.7 0.055 0.063 0.029 22.8 4.4 37813
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.69 100 0.487 0.264
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 4HRQ 1.66 36.33 35915 1889 99.97 0.16139 0.15975 0.19291 0.1897 RANDOM 20.831
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.431 r_dihedral_angle_4_deg 15.988 r_dihedral_angle_3_deg 12.07 r_dihedral_angle_1_deg 6.339 r_long_range_B_refined 5.787 r_long_range_B_other 5.778 r_scangle_other 4.285 r_scbond_it 2.957 r_scbond_other 2.957 r_mcangle_it 2.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.431 r_dihedral_angle_4_deg 15.988 r_dihedral_angle_3_deg 12.07 r_dihedral_angle_1_deg 6.339 r_long_range_B_refined 5.787 r_long_range_B_other 5.778 r_scangle_other 4.285 r_scbond_it 2.957 r_scbond_other 2.957 r_mcangle_it 2.899 r_mcangle_other 2.899 r_mcbond_it 1.942 r_mcbond_other 1.936 r_angle_refined_deg 1.678 r_angle_other_deg 1.55 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2666 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing