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PaMurU in complex with Ca2+ and UTP substrate
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 2.39 48.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.501 α = 90.904 b = 51.644 β = 91.283 c = 71.851 γ = 102.214
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 0.96769 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 1.8 71.82 85.6 0.15 0.989 4.9 3.7 57440
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 1.8 1.84 94.6 1.403 0.565 0.8 3.9
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 1.8 50.515 57440 2868 85.638 0.231 0.2289 0.2366 0.2654 0.2695 31.772
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] -0.285 -0.087 1.718 -0.108 2.51 0.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.122 r_dihedral_angle_3_deg 13.106 r_dihedral_angle_2_deg 7.648 r_dihedral_angle_1_deg 6.856 r_lrange_it 5.999 r_lrange_other 5.969 r_scangle_it 4.236 r_scangle_other 4.235 r_mcangle_other 3.317 r_mcangle_it 3.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.122 r_dihedral_angle_3_deg 13.106 r_dihedral_angle_2_deg 7.648 r_dihedral_angle_1_deg 6.856 r_lrange_it 5.999 r_lrange_other 5.969 r_scangle_it 4.236 r_scangle_other 4.235 r_mcangle_other 3.317 r_mcangle_it 3.316 r_scbond_it 2.723 r_scbond_other 2.723 r_mcbond_it 2.247 r_mcbond_other 2.244 r_angle_refined_deg 1.648 r_angle_other_deg 0.567 r_nbd_refined 0.223 r_metal_ion_refined 0.213 r_symmetry_nbd_other 0.212 r_nbd_other 0.177 r_nbtor_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.175 r_xyhbond_nbd_refined 0.164 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.08 r_symmetry_nbd_refined 0.072 r_symmetry_xyhbond_nbd_other 0.029 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_xyhbond_nbd_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5121 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing