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Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FWN PDB Entry 1FWN
Crystallization Crystal Properties Matthews coefficient Solvent content 2.76 55.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.466 α = 90 b = 84.466 β = 90 c = 159.907 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54180
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 33 99.7 0.128 0.128 3.4 6.4 62022 61836 2 18.5
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 (Observed) 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 PDB Entry 1FWN 1.8 30.16 61836 6014 99.7 0.234 0.234 0.2383 0.268 0.2709 RANDOM 37.2
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] 4.07 2.86 4.07 -8.15
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_scangle_it 3.8 c_scbond_it 2.81 c_mcangle_it 2.49 c_mcbond_it 1.78 c_angle_deg 1.6 c_improper_angle_d 0.86 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_scangle_it 3.8 c_scbond_it 2.81 c_mcangle_it 2.49 c_mcbond_it 1.78 c_angle_deg 1.6 c_improper_angle_d 0.86 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4125 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 48
Software Software Software Name Purpose CNS refinement