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Structure of beta-1,2-glucanase from Photobacterium gaetbulicola (PgSGL3, ligand-free)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 HEPES, MgCl2, PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.93 36.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.284 α = 90 b = 76.595 β = 90 c = 94.425 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 PILATUS3 S 2M 2019-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.2 47.213 96 0.096 0.06 0.993 11.6 6.4 114009
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 1.2 1.22 91.5 0.433 0.271 0.904 4 6.6
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) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 1.2 47.213 113930 5667 95.77 0.192 0.1913 0.2007 0.208 0.2176 11.085
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] 0.008 -0.007 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.543 r_dihedral_angle_3_deg 14.693 r_dihedral_angle_2_deg 9.845 r_dihedral_angle_1_deg 6.484 r_lrange_it 3.862 r_lrange_other 3.809 r_scangle_it 3.074 r_scangle_other 3.074 r_scbond_it 2.044 r_scbond_other 2.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.543 r_dihedral_angle_3_deg 14.693 r_dihedral_angle_2_deg 9.845 r_dihedral_angle_1_deg 6.484 r_lrange_it 3.862 r_lrange_other 3.809 r_scangle_it 3.074 r_scangle_other 3.074 r_scbond_it 2.044 r_scbond_other 2.044 r_angle_refined_deg 1.94 r_mcangle_it 1.803 r_mcangle_other 1.803 r_mcbond_it 1.218 r_mcbond_other 1.218 r_angle_other_deg 1.083 r_nbd_other 0.247 r_nbd_refined 0.228 r_symmetry_nbd_refined 0.212 r_nbtor_refined 0.2 r_symmetry_nbd_other 0.197 r_symmetry_xyhbond_nbd_refined 0.114 r_chiral_restr 0.112 r_xyhbond_nbd_refined 0.106 r_symmetry_nbtor_other 0.084 r_gen_planes_other 0.017 r_gen_planes_refined 0.014 r_bond_refined_d 0.013 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3415 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling CRANK2 phasing