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Crystal structure of a recombinant Vatairea macrocarpa seed lectin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U2A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 Cubic-like crystals
Crystal Properties Matthews coefficient Solvent content 2.06 40.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.083 α = 90 b = 96.083 β = 90 c = 85.099 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 PIXEL DECTRIS PILATUS 6M 2013-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.915 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.898 83.21 99.9 0.039 0.041 0.013 31 9.9 36249 36249
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) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 99.6 0.227 0.227 0.077 3.4 9.6 5239
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 4U2A 1.9 83.21 36221 1764 99.9 0.1937 0.1916 0.1991 0.2352 0.2364 RANDOM 33.963
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] -0.71 -0.36 -0.71 2.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.394 r_dihedral_angle_4_deg 17.487 r_dihedral_angle_3_deg 14.834 r_dihedral_angle_1_deg 6.982 r_mcangle_it 2.144 r_angle_refined_deg 1.942 r_mcbond_other 1.779 r_mcbond_it 1.778 r_angle_other_deg 0.876 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.394 r_dihedral_angle_4_deg 17.487 r_dihedral_angle_3_deg 14.834 r_dihedral_angle_1_deg 6.982 r_mcangle_it 2.144 r_angle_refined_deg 1.942 r_mcbond_other 1.779 r_mcbond_it 1.778 r_angle_other_deg 0.876 r_chiral_restr 0.118 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3620 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SCALA data scaling PHASER phasing MOSFLM data reduction