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Structure of pea lectin in complex with alpha-methyl-D-glucopyranoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2LTN PDB ENTRY 2LTN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 1.7 M AMMONIUM SULFATE, 10% (V/V) ETHANOL, pH 7.00
Crystal Properties Matthews coefficient Solvent content 1.94 36.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.793 α = 90 b = 61.235 β = 90 c = 136.005 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 293 IMAGE PLATE MARRESEARCH MIRRORS 2002-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ELLIOTT GX-6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2 30 95.4 0.058 17.9 2.8 30005 28.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 83.5 0.42 1.92 2.19
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2LTN 2.09 27.95 23508 1181 98.3 0.165 0.163 0.1648 0.209 RANDOM 22.77
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] 0.46 -0.09 -0.36
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.794 r_dihedral_angle_1_deg 2.936 r_scbond_it 2.532 r_mcangle_it 1.867 r_angle_refined_deg 1.305 r_mcbond_it 1.02 r_nbd_refined 0.235 r_symmetry_vdw_refined 0.191 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.141
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.794 r_dihedral_angle_1_deg 2.936 r_scbond_it 2.532 r_mcangle_it 1.867 r_angle_refined_deg 1.305 r_mcbond_it 1.02 r_nbd_refined 0.235 r_symmetry_vdw_refined 0.191 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.1 r_metal_ion_refined 0.068 r_gen_planes_refined 0.01 r_bond_refined_d 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3576 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing