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1,6-anhydro-n-actetylmuramic acid kinase (AnmK) in complex with AMPPNP, and AnhMurNAc at 1.7 Angstroms resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QBW same protein
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 2.58 52.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.67 α = 90 b = 90.67 β = 90 c = 171.686 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) 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 1.7 46.25 100 0.24 0.99 17.4 20.7 87575
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 1.7 1.73 100 0.398 0.81 1.9 20.9
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 1.7 46.249 87521 4235 99.979 0.171 0.1689 0.1754 0.2046 0.2042 28.328
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] 5.196 5.196 -10.392
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.12 r_dihedral_angle_3_deg 13.747 r_dihedral_angle_1_deg 6.385 r_dihedral_angle_2_deg 5.396 r_lrange_it 3.591 r_lrange_other 3.553 r_scangle_it 2.296 r_scangle_other 2.296 r_mcangle_it 1.964 r_mcangle_other 1.964
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.12 r_dihedral_angle_3_deg 13.747 r_dihedral_angle_1_deg 6.385 r_dihedral_angle_2_deg 5.396 r_lrange_it 3.591 r_lrange_other 3.553 r_scangle_it 2.296 r_scangle_other 2.296 r_mcangle_it 1.964 r_mcangle_other 1.964 r_scbond_it 1.515 r_scbond_other 1.515 r_mcbond_it 1.285 r_mcbond_other 1.284 r_angle_refined_deg 1.071 r_angle_other_deg 0.707 r_nbd_other 0.249 r_nbd_refined 0.213 r_symmetry_nbd_refined 0.203 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.142 r_chiral_restr_other 0.141 r_symmetry_xyhbond_nbd_refined 0.127 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.055 r_bond_other_d 0.017 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5494 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 132
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement