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Anoxybacillus ayderensis BglA9 glucose complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AHX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 20%w/v PEG4000, 20%v/v 2-propanol,
0.1 M Na citrate pH5.5
Crystal Properties Matthews coefficient Solvent content 2.22 44.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.513 α = 90 b = 67.828 β = 90 c = 112.411 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 EIGER X 16M 2024-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.6 58.1 93.8 0.119 0.124 0.035 0.999 13.4 11.2 55786
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.7 1.491 1.678 0.753 0.377 0.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.6 58.1 53737 1986 93.751 0.163 0.162 0.173 0.1918 0.2067 random 23.413
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] 0.275 -0.29 0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.124 r_dihedral_angle_3_deg 13.211 r_dihedral_angle_1_deg 6.654 r_lrange_it 6.558 r_lrange_other 6.508 r_dihedral_angle_2_deg 6.338 r_scangle_it 5.454 r_scangle_other 5.453 r_scbond_it 3.599 r_scbond_other 3.598
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.124 r_dihedral_angle_3_deg 13.211 r_dihedral_angle_1_deg 6.654 r_lrange_it 6.558 r_lrange_other 6.508 r_dihedral_angle_2_deg 6.338 r_scangle_it 5.454 r_scangle_other 5.453 r_scbond_it 3.599 r_scbond_other 3.598 r_mcangle_other 2.395 r_mcangle_it 2.391 r_angle_refined_deg 2.3 r_mcbond_other 1.752 r_mcbond_it 1.751 r_angle_other_deg 0.802 r_metal_ion_refined 0.354 r_nbd_refined 0.231 r_symmetry_nbd_refined 0.218 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.198 r_nbd_other 0.178 r_symmetry_xyhbond_nbd_refined 0.148 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.12 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3716 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing