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X-ray structure of Paenibacillus kribbensis D-allulose-6-phosphate 3-epimerase
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 293 100 mM Sodium citrate tribasic dihydrate pH 5.5, 38% v/v Polyethylene glycol 200
Crystal Properties Matthews coefficient Solvent content 2.09 41.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.14 α = 90 b = 73.14 β = 90 c = 227.71 γ = 120
Symmetry Space Group P 32 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 100 PIXEL DECTRIS PILATUS3 6M 2023-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
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 1.46 48.68 97.9 0.052 0.999 20.7 9.5 121091
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 1.46 1.5 0.892 0.888
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 1.46 48.68 114945 6121 97.92 0.21162 0.21059 0.2201 0.231 0.2406 RANDOM 21.303
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] -0.06 -0.03 -0.06 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.03 r_dihedral_angle_2_deg 9.8 r_dihedral_angle_1_deg 8.422 r_long_range_B_refined 6.311 r_long_range_B_other 6.296 r_scangle_other 5.736 r_scbond_it 4.073 r_scbond_other 4.07 r_mcangle_other 2.558 r_mcangle_it 2.556
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.03 r_dihedral_angle_2_deg 9.8 r_dihedral_angle_1_deg 8.422 r_long_range_B_refined 6.311 r_long_range_B_other 6.296 r_scangle_other 5.736 r_scbond_it 4.073 r_scbond_other 4.07 r_mcangle_other 2.558 r_mcangle_it 2.556 r_mcbond_it 2.06 r_mcbond_other 2.06 r_angle_other_deg 1.207 r_angle_refined_deg 0.752 r_chiral_restr 0.041 r_bond_refined_d 0.004 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 5295 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing