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Structure of beta-1,2-glucanase from Xanthomonas campestris pv. campestris (beta-1,2-glucoheptasaccharide complex)-E239Q mutant
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, HANGING DROP 293 NaNO3, PEG 3350, Bis-tris propane
Crystal Properties Matthews coefficient Solvent content 7.21 82.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 220.178 α = 90 b = 220.178 β = 90 c = 220.178 γ = 90
Symmetry Space Group P 43 3 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 PILATUS 6M 2022-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.45 49.233 100 0.121 0.027 1 33.7 39.1 67208
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.51 1.05 0.233 0.949 5
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 49.233 63225 3168 99.896 0.339 0.3381 0.3421 0.3646 0.3678 41.267
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.365 r_dihedral_angle_6_deg 16.202 r_dihedral_angle_1_deg 7.088 r_lrange_it 6.194 r_lrange_other 6.194 r_dihedral_angle_2_deg 6.057 r_scangle_it 4.946 r_scangle_other 4.945 r_mcangle_other 4.495 r_mcangle_it 4.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.365 r_dihedral_angle_6_deg 16.202 r_dihedral_angle_1_deg 7.088 r_lrange_it 6.194 r_lrange_other 6.194 r_dihedral_angle_2_deg 6.057 r_scangle_it 4.946 r_scangle_other 4.945 r_mcangle_other 4.495 r_mcangle_it 4.491 r_scbond_it 3.539 r_scbond_other 3.538 r_mcbond_it 3.141 r_mcbond_other 3.124 r_angle_refined_deg 2.011 r_angle_other_deg 0.822 r_nbd_refined 0.284 r_symmetry_nbd_other 0.216 r_symmetry_nbd_refined 0.208 r_nbtor_refined 0.193 r_xyhbond_nbd_refined 0.183 r_nbd_other 0.161 r_chiral_restr 0.146 r_symmetry_xyhbond_nbd_refined 0.11 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.059 r_gen_planes_other 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_chiral_restr_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3620 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing