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Polysaccharide lyase BcPL33HA (BcellWH2_04512) Apo form
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, SITTING DROP 7.5 295 10 % PEG 8000
8 % Ethylene glycol
0.1 M HEPES pH 7.5
28 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.6 52.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.63 α = 90 b = 91.39 β = 109.28 c = 84.77 γ = 90
Symmetry Space Group C 1 2 1
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 2023-03-23 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) 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 2.11 40.01 99.7 1 10.8 6.7 42837
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 2.11 2.17 0.7 1.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.11 40.008 42836 2098 99.721 0.192 0.1888 0.2502 0.2399 42.933
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] 0.029 0.781 1.831 -1.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.934 r_dihedral_angle_3_deg 14.869 r_dihedral_angle_2_deg 11.723 r_lrange_other 7.966 r_lrange_it 7.955 r_dihedral_angle_1_deg 7.155 r_scangle_it 6.721 r_scangle_other 6.721 r_mcangle_other 4.813 r_mcangle_it 4.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.934 r_dihedral_angle_3_deg 14.869 r_dihedral_angle_2_deg 11.723 r_lrange_other 7.966 r_lrange_it 7.955 r_dihedral_angle_1_deg 7.155 r_scangle_it 6.721 r_scangle_other 6.721 r_mcangle_other 4.813 r_mcangle_it 4.812 r_scbond_it 4.791 r_scbond_other 4.79 r_mcbond_it 3.774 r_mcbond_other 3.771 r_angle_refined_deg 1.826 r_angle_other_deg 0.613 r_nbd_refined 0.215 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.188 r_symmetry_xyhbond_nbd_refined 0.16 r_xyhbond_nbd_refined 0.156 r_symmetry_nbd_refined 0.153 r_nbd_other 0.138 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.081 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4981 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing