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Crystallization and structural characterization of phosphopentomutase from the hyperthermophilic archaeon Thermococcus kodakarensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q6I7B6-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% v/v PEG300, 10% v/v Glycerol, 0.1 M Tris-HCl- pH 8.5, 5% w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 2.51 51.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.772 α = 90 b = 97.575 β = 94 c = 128.15 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 4M 2023-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.90 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.39 50 98.9 0.125 0.135 0.998 10.48 7 77057
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.39 2.53 97 1.039 0.5 0.7 1.57 6.8
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 (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 2.39 50 74699 2310 99.01 0.2033 0.20111 0.2067 0.27378 0.2707 RANDOM 50.494
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] 0.52 0.53 0.49 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.996 r_dihedral_angle_4_deg 20.915 r_dihedral_angle_3_deg 19.151 r_long_range_B_other 10.838 r_long_range_B_refined 10.833 r_dihedral_angle_1_deg 8.012 r_scangle_other 7.916 r_mcangle_other 6.676 r_mcangle_it 6.675 r_scbond_it 5.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.996 r_dihedral_angle_4_deg 20.915 r_dihedral_angle_3_deg 19.151 r_long_range_B_other 10.838 r_long_range_B_refined 10.833 r_dihedral_angle_1_deg 8.012 r_scangle_other 7.916 r_mcangle_other 6.676 r_mcangle_it 6.675 r_scbond_it 5.222 r_scbond_other 5.221 r_mcbond_it 4.612 r_mcbond_other 4.608 r_angle_refined_deg 1.721 r_angle_other_deg 1.266 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13803 Nucleic Acid Atoms Solvent Atoms 419 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data scaling PHASER phasing XDS data reduction