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Photorhabdus asymbiotica lectin (PHL) in free form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C9O
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 2.69 54.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.235 α = 90 b = 81.235 β = 90 c = 113.441 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 RIGAKU SATURN 944+ 2014-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 44.16 98.8 0.071 0.997 14.7 3.6 34331
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 93.4 0.237 0.934 2.5
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 5C9O 1.9 44.16 32591 1702 98.77 0.1676 0.16638 0.176 0.19101 0.1941 RANDOM 12.541
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] 0.04 0.02 0.04 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.247 r_dihedral_angle_3_deg 11.121 r_dihedral_angle_4_deg 8.28 r_dihedral_angle_1_deg 7.698 r_long_range_B_refined 3.908 r_long_range_B_other 3.242 r_angle_refined_deg 1.308 r_scangle_other 1.17 r_mcangle_it 1.126 r_mcangle_other 1.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.247 r_dihedral_angle_3_deg 11.121 r_dihedral_angle_4_deg 8.28 r_dihedral_angle_1_deg 7.698 r_long_range_B_refined 3.908 r_long_range_B_other 3.242 r_angle_refined_deg 1.308 r_scangle_other 1.17 r_mcangle_it 1.126 r_mcangle_other 1.125 r_angle_other_deg 0.953 r_scbond_it 0.709 r_scbond_other 0.709 r_mcbond_other 0.65 r_mcbond_it 0.649 r_chiral_restr 0.093 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 2664 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing