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Crystal structure of a lectin from Canavalia brasiliensis seed (ConBr) complexed with alpha-aminobutyric acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AZD PDB ENTRY 1AZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 1.8 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.43 49.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.323 α = 90 b = 73.02 β = 90 c = 99.542 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 2008-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.42 LNLS D03B-MX1
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 1.775 58.93 0.069 14784
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 2.1 2.21 0.196 11019
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 PDB ENTRY 1AZD 2.1 36.51 14017 749 99.15 0.20676 0.20433 0.2045 0.25268 0.2565 RANDOM 28.543
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] 0.02 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.252 r_dihedral_angle_3_deg 13.992 r_dihedral_angle_4_deg 12.018 r_dihedral_angle_1_deg 9.771 r_scangle_it 3.089 r_scbond_it 2.333 r_angle_refined_deg 1.719 r_mcangle_it 1.569 r_mcbond_it 1.101 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.252 r_dihedral_angle_3_deg 13.992 r_dihedral_angle_4_deg 12.018 r_dihedral_angle_1_deg 9.771 r_scangle_it 3.089 r_scbond_it 2.333 r_angle_refined_deg 1.719 r_mcangle_it 1.569 r_mcbond_it 1.101 r_nbtor_refined 0.303 r_chiral_restr 0.243 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.203 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.18 r_metal_ion_refined 0.069 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1807 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 17
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling