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Structure of Narcissus pseudonarcissus lectin complex with Mannobiose at 1.7 A resolution, form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NPL PDB ENTRY 1NPL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 293 10 mg/ml in Phosphate buffered saline, containing up to 20mM beta-1,3 mannobiose, pH 8.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.8 56.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.003 α = 90 b = 102.011 β = 90 c = 74.366 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 IMAGE PLATE MAR scanner 300 mm plate MIRROR 1996-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.7 21.031 99.2 0.077 0.077 3 30200
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 99.2 0.382 0.382 1.8 3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NPL 1.7 21.031 30180 1523 98.96 0.18823 0.18684 0.21279 0.246 RANDOM 18.66
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 -0.78 1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.49 r_dihedral_angle_3_deg 7.953 r_dihedral_angle_4_deg 5.777 r_scangle_it 4.649 r_scbond_it 3.238 r_dihedral_angle_1_deg 2.606 r_angle_other_deg 2.461 r_mcangle_it 2.199 r_mcbond_it 1.91 r_angle_refined_deg 1.544
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.49 r_dihedral_angle_3_deg 7.953 r_dihedral_angle_4_deg 5.777 r_scangle_it 4.649 r_scbond_it 3.238 r_dihedral_angle_1_deg 2.606 r_angle_other_deg 2.461 r_mcangle_it 2.199 r_mcbond_it 1.91 r_angle_refined_deg 1.544 r_mcbond_other 0.54 r_symmetry_hbond_refined 0.289 r_nbd_other 0.175 r_symmetry_vdw_other 0.172 r_nbtor_refined 0.158 r_nbd_refined 0.157 r_xyhbond_nbd_refined 0.145 r_nbtor_other 0.096 r_chiral_restr 0.095 r_symmetry_vdw_refined 0.067 r_bond_refined_d 0.018 r_xyhbond_nbd_other 0.013 r_bond_other_d 0.004 r_gen_planes_refined 0.003 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1716 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 163
Software Software Software Name Purpose SCALA data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction