☰ Navigation Tabs
Crystal structure of Canavalia virosa lectin in complex with alpha-methyl-mannoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OW4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 300 Tris-HCl, Ammonium sulphate, Glycerol
Crystal Properties Matthews coefficient Solvent content 2.1 41.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.25 α = 90 b = 81.74 β = 90 c = 86.93 γ = 90
Symmetry Space Group P 21 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 100 PIXEL DECTRIS PILATUS 2M 2014-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.47 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.49 36.99 94.5 0.083 0.083 0.095 0.045 0.989 12.2 4.6 14676 14676
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.49 2.63 68.6 0.174 0.074 0.041 0.95 6.2 4 1518
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 2OW4 2.52 36.99 13883 754 97.48 0.1879 0.1845 0.1942 0.2509 0.2538 RANDOM 27.912
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] 0.03 -0.05 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.079 r_dihedral_angle_4_deg 17.629 r_dihedral_angle_3_deg 14.597 r_dihedral_angle_1_deg 6.895 r_angle_other_deg 3.806 r_mcangle_it 3.44 r_mcbond_it 2.067 r_mcbond_other 2.063 r_angle_refined_deg 1.663 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.079 r_dihedral_angle_4_deg 17.629 r_dihedral_angle_3_deg 14.597 r_dihedral_angle_1_deg 6.895 r_angle_other_deg 3.806 r_mcangle_it 3.44 r_mcbond_it 2.067 r_mcbond_other 2.063 r_angle_refined_deg 1.663 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_other 0.011 r_gen_planes_refined 0.009 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3588 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing