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1,6-anhydro-n-actetylmuramic acid kinase (AnmK)in complex with non-hydrolyzable AMPPNP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 20% PEG 3350, Na/K tartrate 0.2M
Crystal Properties Matthews coefficient Solvent content 2.62 54.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.94 α = 90 b = 89.94 β = 90 c = 176.958 γ = 120
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 PILATUS 6M 2022-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
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 2.2 47.024 100 0.099 0.999 21 20.8 41089
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 100 1.717 0.701 2.2 21.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.2 47.024 41048 2042 99.981 0.186 0.1833 0.2206 0.231 0.2799 53.71
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] 0.845 0.845 -1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.519 r_dihedral_angle_6_deg 14.294 r_dihedral_angle_1_deg 7.277 r_lrange_it 6.944 r_lrange_other 6.932 r_dihedral_angle_2_deg 5.784 r_mcangle_it 4.822 r_mcangle_other 4.822 r_scangle_it 4.69 r_scangle_other 4.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.519 r_dihedral_angle_6_deg 14.294 r_dihedral_angle_1_deg 7.277 r_lrange_it 6.944 r_lrange_other 6.932 r_dihedral_angle_2_deg 5.784 r_mcangle_it 4.822 r_mcangle_other 4.822 r_scangle_it 4.69 r_scangle_other 4.69 r_mcbond_it 3.387 r_mcbond_other 3.385 r_scbond_it 3.276 r_scbond_other 3.275 r_angle_refined_deg 1.159 r_angle_other_deg 0.64 r_nbd_other 0.236 r_symmetry_xyhbond_nbd_refined 0.236 r_nbd_refined 0.221 r_symmetry_nbd_other 0.196 r_xyhbond_nbd_refined 0.177 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.166 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.058 r_metal_ion_refined 0.042 r_bond_other_d 0.015 r_symmetry_xyhbond_nbd_other 0.008 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5401 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing