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PaMurU in complex with Mn2+ 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 2.46 50.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.943 α = 89.885 b = 51.957 β = 89.557 c = 73.117 γ = 77.559
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 2025-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.7712 ALBA XALOC
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 2.1 50.74 93.8 0.121 0.978 8.3 3.5 40882
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 2.1 2.16 89.9 0.423 0.708 1.3 3.5
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 2.1 50.74 40875 1921 93.827 0.204 0.2012 0.2093 0.2515 0.2581 28.569
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] 0.399 0.503 -1.098 -0.169 0.945 -0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.341 r_dihedral_angle_3_deg 12.941 r_dihedral_angle_2_deg 7.098 r_dihedral_angle_1_deg 6.997 r_lrange_other 6.037 r_lrange_it 6.035 r_scangle_it 4.104 r_scangle_other 4.104 r_mcangle_it 3.441 r_mcangle_other 3.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.341 r_dihedral_angle_3_deg 12.941 r_dihedral_angle_2_deg 7.098 r_dihedral_angle_1_deg 6.997 r_lrange_other 6.037 r_lrange_it 6.035 r_scangle_it 4.104 r_scangle_other 4.104 r_mcangle_it 3.441 r_mcangle_other 3.441 r_scbond_it 2.631 r_scbond_other 2.631 r_mcbond_it 2.224 r_mcbond_other 2.221 r_angle_refined_deg 1.732 r_angle_other_deg 0.562 r_nbd_refined 0.223 r_symmetry_nbd_other 0.204 r_nbd_other 0.196 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.168 r_symmetry_nbd_refined 0.092 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_xyhbond_nbd_other 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 5122 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing