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1,6-anhydro-n-actetylmuramic acid kinase (AnmK)
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 7.5 291 8% PEG 8000, 0.2M litium chloride, 0.05M magnesium sulfate.
Crystal Properties Matthews coefficient Solvent content 2.67 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.093 α = 90 b = 90.093 β = 90 c = 178.378 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 2022-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979264 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 47.292 100 1 22.5 20.1 55214
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 2.05 100 1.688 0.667 2.1 20.5
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 (All) 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 3QBX 2 47.292 55167 2667 99.978 0.179 0.1776 0.2011 0.2121 0.2405 RANDOM 51.715
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] -0.319 -0.319 0.638
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.426 r_dihedral_angle_6_deg 13.452 r_dihedral_angle_1_deg 6.299 r_lrange_it 5.524 r_lrange_other 5.487 r_dihedral_angle_2_deg 5.367 r_mcangle_it 3.525 r_mcangle_other 3.524 r_scangle_it 3.522 r_scangle_other 3.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.426 r_dihedral_angle_6_deg 13.452 r_dihedral_angle_1_deg 6.299 r_lrange_it 5.524 r_lrange_other 5.487 r_dihedral_angle_2_deg 5.367 r_mcangle_it 3.525 r_mcangle_other 3.524 r_scangle_it 3.522 r_scangle_other 3.522 r_mcbond_it 2.437 r_mcbond_other 2.437 r_scbond_it 2.409 r_scbond_other 2.408 r_angle_refined_deg 1.04 r_angle_other_deg 0.473 r_nbd_refined 0.21 r_symmetry_nbd_other 0.189 r_nbd_other 0.187 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.151 r_symmetry_xyhbond_nbd_other 0.141 r_symmetry_nbd_refined 0.126 r_symmetry_xyhbond_nbd_refined 0.122 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.055 r_bond_other_d 0.009 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 5413 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing