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Photorhabdus asymbiotica lectin PHL in complex with L-rhamnose
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, HANGING DROP 7.5 293 3.8 M NaCl, 100 mM Hepes, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.86 56.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.499 α = 90 b = 80.499 β = 90 c = 113.413 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 CCD MARMOSAIC 300 mm CCD 2016-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.3 0.8943 BESSY 14.3
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 1.89 43.99 99.8 0.113 0.999 16.1 12.2 34618 25.4
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 1.89 1.99 98.6 1.317 0.742 2 12.1
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 1.89 43.99 32866 1712 99.77 0.20113 0.19967 0.2057 0.22876 0.2356 RANDOM 30.646
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] 0.7 0.35 0.7 -2.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.333 r_dihedral_angle_3_deg 11.546 r_dihedral_angle_4_deg 9.211 r_dihedral_angle_1_deg 8.619 r_long_range_B_refined 4.166 r_long_range_B_other 4.087 r_scangle_other 2.639 r_mcangle_it 2.581 r_mcangle_other 2.58 r_mcbond_it 1.742
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.333 r_dihedral_angle_3_deg 11.546 r_dihedral_angle_4_deg 9.211 r_dihedral_angle_1_deg 8.619 r_long_range_B_refined 4.166 r_long_range_B_other 4.087 r_scangle_other 2.639 r_mcangle_it 2.581 r_mcangle_other 2.58 r_mcbond_it 1.742 r_mcbond_other 1.742 r_scbond_it 1.739 r_scbond_other 1.739 r_angle_refined_deg 1.309 r_angle_other_deg 1.249 r_chiral_restr 0.052 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 2633 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing