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Crystal structure of ClAgl29B bound with L-glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XSG Apo form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 293 0.1 M sodium citrate (pH 3.5), 5% PEG 20,000, 5% 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.72 54.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.393 α = 90 b = 121.583 β = 90 c = 166.372 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 PILATUS 2M 2021-03-05 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 Sym I (Observed) Rrim 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 1.708 98.164 99.8 0.093 0.101 0.999 17.44 6.7 159024 27.15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.71 1.81 99.1 0.863 0.942 0.81 2.37 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE Apo form 1.708 46.598 159021 7948 99.827 0.18 0.1789 0.1899 0.2016 0.2119 24.522
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] 0.261 1.425 -1.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.146 r_dihedral_angle_3_deg 14.408 r_dihedral_angle_2_deg 13.178 r_dihedral_angle_1_deg 6.564 r_lrange_it 5.579 r_lrange_other 5.491 r_scangle_it 4.086 r_scangle_other 4.086 r_mcangle_it 3.083 r_mcangle_other 3.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.146 r_dihedral_angle_3_deg 14.408 r_dihedral_angle_2_deg 13.178 r_dihedral_angle_1_deg 6.564 r_lrange_it 5.579 r_lrange_other 5.491 r_scangle_it 4.086 r_scangle_other 4.086 r_mcangle_it 3.083 r_mcangle_other 3.083 r_scbond_it 2.655 r_scbond_other 2.654 r_mcbond_it 2.076 r_mcbond_other 2.075 r_angle_refined_deg 1.287 r_angle_other_deg 0.453 r_symmetry_nbd_refined 0.276 r_nbd_other 0.219 r_nbd_refined 0.212 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.172 r_xyhbond_nbd_refined 0.125 r_metal_ion_refined 0.119 r_ncsr_local_group_1 0.09 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8872 Nucleic Acid Atoms Solvent Atoms 692 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing