☰ Navigation Tabs
X-ray structure of Paenibacillus kribbensis D-ribose-5-phosphate isomerase B
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 BIS-TRIS pH 6.5, 20% w/v Polyethylene glycol 1,500
Crystal Properties Matthews coefficient Solvent content 2.13 42.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.33 α = 90 b = 65.1 β = 90 c = 166.94 γ = 90
Symmetry Space Group P 21 21 21
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 2022-06-28 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 1.94 47.3 98 0.067 0.998 18.5 6.3 46052
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 1.94 1.99 0.529 0.889
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 1.94 47.3 43646 2349 97.52 0.24112 0.23969 0.2484 0.26802 0.2758 RANDOM 31.172
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] -0.26 -0.11 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.332 r_long_range_B_other 9.584 r_long_range_B_refined 9.572 r_scangle_other 7.961 r_dihedral_angle_1_deg 7.862 r_dihedral_angle_2_deg 7.58 r_scbond_it 6.062 r_scbond_other 5.98 r_mcangle_it 3.893 r_mcangle_other 3.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.332 r_long_range_B_other 9.584 r_long_range_B_refined 9.572 r_scangle_other 7.961 r_dihedral_angle_1_deg 7.862 r_dihedral_angle_2_deg 7.58 r_scbond_it 6.062 r_scbond_other 5.98 r_mcangle_it 3.893 r_mcangle_other 3.893 r_mcbond_it 3.275 r_mcbond_other 3.257 r_angle_refined_deg 0.56 r_angle_other_deg 0.227 r_chiral_restr 0.031 r_bond_refined_d 0.001 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 4444 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing