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Monomeric structure of concanavalin A at pH 7.5 from Carnivalia ensiformis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C57
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 PEK6K, MPD in HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.26 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.303 α = 90 b = 86.59 β = 90 c = 89.511 γ = 90
Symmetry Space Group I 2 2 2
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 QUANTUM 270 2017-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.000 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 44.76 98.8 28.2 6.9 32123
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.68 92.8
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 1C57 1.6 44.76 30527 1587 98.65 0.1673 0.16584 0.1654 0.19648 0.1971 RANDOM 19.108
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 0.41 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.518 r_dihedral_angle_4_deg 15.443 r_dihedral_angle_3_deg 13.185 r_dihedral_angle_1_deg 7.398 r_long_range_B_refined 5.63 r_scbond_it 3.325 r_mcangle_it 2.665 r_angle_refined_deg 2.326 r_mcbond_it 1.83 r_chiral_restr 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.518 r_dihedral_angle_4_deg 15.443 r_dihedral_angle_3_deg 13.185 r_dihedral_angle_1_deg 7.398 r_long_range_B_refined 5.63 r_scbond_it 3.325 r_mcangle_it 2.665 r_angle_refined_deg 2.326 r_mcbond_it 1.83 r_chiral_restr 0.204 r_bond_refined_d 0.026 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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_it r_scangle_other 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 1809 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data processing SCALA data scaling PHASER phasing Coot model building