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PaMurU in complex with their natural substrates (UTP and NAM-1P) and Mg2+ cofactor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8HHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 HEPES 0.1M pH=7.5, 0.2M NaCl
25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.41 49.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.567 α = 90.63 b = 51.586 β = 90.531 c = 72.725 γ = 102.618
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 EIGER2 X 9M 2025-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9677 ESRF ID30B
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 1.95 72.72 85.9 0.112 0.992 7.4 3.6 45729
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 1.95 2 94.1 0.587 0.819 2.3 3.7
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 1.951 72.715 45725 2392 85.873 0.222 0.22 0.2264 0.2662 0.272 24.637
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] -0.247 -0.346 1.391 0.765 1.208 -0.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.432 r_dihedral_angle_3_deg 12.735 r_dihedral_angle_2_deg 7.224 r_dihedral_angle_1_deg 7.053 r_lrange_it 4.593 r_lrange_other 4.578 r_scangle_it 3.396 r_scangle_other 3.389 r_mcangle_other 2.453 r_mcangle_it 2.452
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.432 r_dihedral_angle_3_deg 12.735 r_dihedral_angle_2_deg 7.224 r_dihedral_angle_1_deg 7.053 r_lrange_it 4.593 r_lrange_other 4.578 r_scangle_it 3.396 r_scangle_other 3.389 r_mcangle_other 2.453 r_mcangle_it 2.452 r_scbond_it 2.127 r_scbond_other 2.119 r_angle_refined_deg 1.669 r_mcbond_it 1.589 r_mcbond_other 1.589 r_angle_other_deg 0.561 r_nbd_refined 0.214 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.174 r_nbd_other 0.172 r_xyhbond_nbd_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.144 r_symmetry_nbd_refined 0.116 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.078 r_metal_ion_refined 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5106 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 165
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing