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Photorhabdus asymbiotica lectin (PHL) in complex with alpha-methyl fucoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MXE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 3.7-4.3 M NaCl, 100 mM Hepes pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.68 54.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.249 α = 90 b = 81.249 β = 90 c = 113.231 γ = 120
Symmetry Space Group P 31 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 PILATUS 6M 2013-12-06 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) 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 1.9 44.11 100 0.076 0.999 22.4 10.7 34705
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 100 0.457 0.945 5.3 11
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 5MXE 1.9 44.11 32917 1746 99.99 0.16871 0.16724 0.1755 0.19573 0.1998 RANDOM 23.486
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] 0.29 0.14 0.29 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.853 r_dihedral_angle_3_deg 10.896 r_dihedral_angle_1_deg 7.742 r_dihedral_angle_4_deg 6.726 r_long_range_B_refined 3.843 r_long_range_B_other 3.423 r_scangle_other 2.022 r_mcangle_it 1.7 r_mcangle_other 1.7 r_angle_refined_deg 1.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.853 r_dihedral_angle_3_deg 10.896 r_dihedral_angle_1_deg 7.742 r_dihedral_angle_4_deg 6.726 r_long_range_B_refined 3.843 r_long_range_B_other 3.423 r_scangle_other 2.022 r_mcangle_it 1.7 r_mcangle_other 1.7 r_angle_refined_deg 1.306 r_scbond_it 1.302 r_scbond_other 1.301 r_mcbond_it 1.124 r_mcbond_other 1.123 r_angle_other_deg 0.936 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.001 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 2672 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing