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X-ray structure of Paenibacillus kribbensis D-allose kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 200 mM Ammonium tartrate dibasic pH6.6, 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.53 51.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.37 α = 90 b = 79.37 β = 90 c = 117.52 γ = 90
Symmetry Space Group P 42 21 2
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 PILATUS3 6M 2022-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.58 47.27 99.9 0.053 0.999 27.5 12.4 52157
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.62 0.83
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 1.58 47.27 49449 2648 99.94 0.17985 0.17883 0.1902 0.19894 0.21 RANDOM 22.871
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] 0.16 0.16 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.704 r_dihedral_angle_1_deg 8.127 r_long_range_B_other 7.124 r_long_range_B_refined 7.12 r_scangle_other 6.081 r_dihedral_angle_2_deg 5.416 r_scbond_it 4.474 r_scbond_other 4.474 r_mcangle_it 3.055 r_mcangle_other 3.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.704 r_dihedral_angle_1_deg 8.127 r_long_range_B_other 7.124 r_long_range_B_refined 7.12 r_scangle_other 6.081 r_dihedral_angle_2_deg 5.416 r_scbond_it 4.474 r_scbond_other 4.474 r_mcangle_it 3.055 r_mcangle_other 3.054 r_mcbond_it 2.348 r_mcbond_other 2.347 r_angle_refined_deg 0.911 r_angle_other_deg 0.333 r_chiral_restr 0.049 r_bond_refined_d 0.002 r_bond_other_d r_dihedral_angle_4_deg r_gen_planes_refined r_gen_planes_other 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 2316 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing