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1.8A Crystal Structure of Psathyrella velutina lectin in complex with N-acetylneuraminic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BWM PDB ENTRY 2BWM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 2.2M (NH4)2SO4, 0.1M MES PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.3 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.728 α = 90 b = 144.403 β = 92.98 c = 52.601 γ = 90
Symmetry Space Group P 1 21 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 ADSC CCD MIRRORS 2005-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.8 24.69 99.8 0.05 8.26 3.93 70971 21.4
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 1.8 1.85 99.8 0.29 1.84 3.87
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 2BWM 1.8 72.17 67358 3575 99.7 0.189 0.186 0.1946 0.231 RANDOM 21.44
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] -0.23 0.11 1.13 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.472 r_dihedral_angle_3_deg 13.873 r_dihedral_angle_4_deg 12.889 r_dihedral_angle_1_deg 6.515 r_scangle_it 3.22 r_scbond_it 2.265 r_angle_refined_deg 1.614 r_mcangle_it 1.526 r_angle_other_deg 1.096 r_mcbond_it 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.472 r_dihedral_angle_3_deg 13.873 r_dihedral_angle_4_deg 12.889 r_dihedral_angle_1_deg 6.515 r_scangle_it 3.22 r_scbond_it 2.265 r_angle_refined_deg 1.614 r_mcangle_it 1.526 r_angle_other_deg 1.096 r_mcbond_it 0.99 r_symmetry_vdw_other 0.241 r_nbd_other 0.199 r_nbd_refined 0.181 r_nbtor_refined 0.177 r_chiral_restr 0.148 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.144 r_symmetry_vdw_refined 0.103 r_nbtor_other 0.086 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 6076 Nucleic Acid Atoms Solvent Atoms 447 Heterogen Atoms 127
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing