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sucrose hydrolase SuxB from Xanthomonas oryzae pv. oryzae in complex with glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9R8I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 285 0.25 M potassium sodium tartrate, 37.5 (w/v) % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.69 54.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.535 α = 90 b = 172.726 β = 90 c = 259.777 γ = 90
Symmetry Space Group I 2 2 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 EIGER X 16M 2025-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.059700 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.95 49.75 100 0.998 11.07 13.2 47939
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 2.95 3.055 0.88
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 2.95 49.75 45465 2468 99.76 0.23277 0.22902 0.2412 0.30182 0.3102 RANDOM 116.981
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] 16.11 -12.03 -4.08
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 23.192 r_long_range_B_refined 23.191 r_dihedral_angle_2_deg 22.427 r_dihedral_angle_3_deg 22.403 r_scangle_other 14.94 r_mcangle_it 14.918 r_mcangle_other 14.918 r_mcbond_it 9.866 r_mcbond_other 9.864 r_scbond_it 9.573
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 23.192 r_long_range_B_refined 23.191 r_dihedral_angle_2_deg 22.427 r_dihedral_angle_3_deg 22.403 r_scangle_other 14.94 r_mcangle_it 14.918 r_mcangle_other 14.918 r_mcbond_it 9.866 r_mcbond_other 9.864 r_scbond_it 9.573 r_scbond_other 9.572 r_dihedral_angle_1_deg 5.468 r_angle_refined_deg 1.088 r_angle_other_deg 0.388 r_chiral_restr 0.049 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 14481 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction Aimless data scaling PHASER phasing