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A CBM32 derived from alginate lyase B (AlyB-OU02)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZU5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 288 1.6M sodium citrate tribasic dihydrate pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.43 49.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.849 α = 90 b = 60.679 β = 90 c = 66.894 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 CMOS RDI CMOS_8M 2017-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 1 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.4 50 100 0.12 21.7 12.5 35712
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.45 0.47
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 (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 5ZU5 1.4 44.94 33822 1786 99.28 0.19023 0.1891 0.189 0.21161 0.2066 RANDOM 14.996
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] -0.02 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.267 r_dihedral_angle_3_deg 11.211 r_dihedral_angle_4_deg 9.317 r_dihedral_angle_1_deg 7.235 r_long_range_B_refined 5.632 r_long_range_B_other 5.39 r_scangle_other 3.392 r_scbond_it 2.293 r_scbond_other 2.291 r_mcangle_it 1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.267 r_dihedral_angle_3_deg 11.211 r_dihedral_angle_4_deg 9.317 r_dihedral_angle_1_deg 7.235 r_long_range_B_refined 5.632 r_long_range_B_other 5.39 r_scangle_other 3.392 r_scbond_it 2.293 r_scbond_other 2.291 r_mcangle_it 1.98 r_mcangle_other 1.979 r_angle_refined_deg 1.876 r_mcbond_other 1.284 r_mcbond_it 1.282 r_angle_other_deg 0.899 r_chiral_restr 0.138 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.004 r_gen_planes_other 0.002 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 1156 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing