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1,6-anhydro-n-actetylmuramic acid kinase (AnmK) in complex with their natural substrates and products
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 6 291 20% PEG 3350, Bis-Tris 0.1 M, pH 6.0, Li2SO4 0.2 M
Crystal Properties Matthews coefficient Solvent content 2.64 53.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.583 α = 90 b = 90.583 β = 90 c = 174.478 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 2022-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979260 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.11 46.764 94.6 0.142 0.041 0.99 18.41 24.8 42080
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.19 64 0.785 0.518 1.555
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.112 46.764 42061 2057 90.69 0.232 0.2303 0.2681 0.1921 RANDOM 48.191
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] -0.136 -0.068 -0.136 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.715 r_dihedral_angle_6_deg 12.609 r_dihedral_angle_2_deg 7.25 r_dihedral_angle_1_deg 5.894 r_lrange_it 4.739 r_lrange_other 4.68 r_mcangle_it 2.941 r_mcangle_other 2.941 r_scangle_it 2.771 r_scangle_other 2.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.715 r_dihedral_angle_6_deg 12.609 r_dihedral_angle_2_deg 7.25 r_dihedral_angle_1_deg 5.894 r_lrange_it 4.739 r_lrange_other 4.68 r_mcangle_it 2.941 r_mcangle_other 2.941 r_scangle_it 2.771 r_scangle_other 2.77 r_mcbond_it 1.79 r_mcbond_other 1.79 r_scbond_it 1.66 r_scbond_other 1.653 r_angle_refined_deg 0.849 r_dihedral_angle_other_2_deg 0.487 r_angle_other_deg 0.289 r_symmetry_nbd_other 0.199 r_nbd_refined 0.195 r_nbtor_refined 0.167 r_nbd_other 0.153 r_symmetry_nbd_refined 0.139 r_xyhbond_nbd_refined 0.13 r_symmetry_xyhbond_nbd_refined 0.105 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.042 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5502 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling PHASER phasing