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Crystal structure of Canavalia brasiliensis (ConBr) complexed with adenine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 1.8 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.27 45.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.12 α = 90 b = 70.94 β = 90 c = 97.43 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 MAR CCD 130 mm 2008-07-25 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.430 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 2 22.56 99 0.067 18.6 9.5 15266
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 2.05 100 0.36 4.8 9.4
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 4H55 2 22.3 15266 806 99.89 0.17805 0.17549 0.1877 0.22797 0.2333 RANDOM 35.118
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] 0.06 -0.08 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.65 r_dihedral_angle_4_deg 20.465 r_sphericity_free 18.132 r_dihedral_angle_3_deg 14.18 r_sphericity_bonded 8.476 r_dihedral_angle_1_deg 8.125 r_rigid_bond_restr 5.776 r_scangle_other 4.435 r_long_range_B_refined 4.269 r_long_range_B_other 4.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.65 r_dihedral_angle_4_deg 20.465 r_sphericity_free 18.132 r_dihedral_angle_3_deg 14.18 r_sphericity_bonded 8.476 r_dihedral_angle_1_deg 8.125 r_rigid_bond_restr 5.776 r_scangle_other 4.435 r_long_range_B_refined 4.269 r_long_range_B_other 4.258 r_scbond_it 4.256 r_scbond_other 4.243 r_mcbond_it 3.95 r_mcbond_other 3.947 r_mcangle_it 3.892 r_mcangle_other 3.891 r_angle_refined_deg 2.001 r_angle_other_deg 0.887 r_chiral_restr 0.111 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1795 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement