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Photorhabdus laumondii subsp. laumondii lectin PLL3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C9P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M NaF, 14% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.86 33.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.582 α = 90 b = 69.416 β = 90 c = 76.706 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 6M 2019-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 1.65 45.53 99.9 0.143 0.143 0.154 0.057 0.997 8.2 7.3 37089 37089
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.74 99.2 0.989 0.06 0.065 0.024 0.708 7.4
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 5C9P 1.65 45.53 35215 1804 99.93 0.1706 0.1693 0.1819 0.196 0.2048 RANDOM 18.29
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] -0.87 -1.12 1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.048 r_dihedral_angle_3_deg 12.909 r_dihedral_angle_4_deg 11.107 r_dihedral_angle_1_deg 8.324 r_angle_refined_deg 1.476 r_angle_other_deg 1.433 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.048 r_dihedral_angle_3_deg 12.909 r_dihedral_angle_4_deg 11.107 r_dihedral_angle_1_deg 8.324 r_angle_refined_deg 1.476 r_angle_other_deg 1.433 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2695 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing