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Crystal structure of a designed Cyanovirin-N homolog lectin; LKAMG in P212121 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HNU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 277 50 mg/ml protein concentration in 0.2 M Li2SO4, 0.1 M Tris-HCl (pH 8.5), and 30% PEG 4000 at protein to mother liquor ratio of 8 to 1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.14 42.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.506 α = 90 b = 46.204 β = 90 c = 50.377 γ = 90
Symmetry Space Group P 21 21 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 CCD RIGAKU SATURN 944 MIRRORS 2006-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT
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 1.35 27.26 97.7 0.039 40.7 13.32 23394 3
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) 1.35 1.4 77.3 0.337 2.7 2.94
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 3HNU 1.37 27.26 21673 1168 99.5 0.17 0.168 0.1621 0.21 0.2033 RANDOM 18.02
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] -0.21 -0.31 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.3 r_dihedral_angle_4_deg 21.589 r_dihedral_angle_3_deg 11.664 r_sphericity_free 9.944 r_dihedral_angle_1_deg 6.984 r_sphericity_bonded 6.211 r_scangle_it 5.815 r_scbond_it 4.038 r_mcangle_it 3.135 r_rigid_bond_restr 2.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.3 r_dihedral_angle_4_deg 21.589 r_dihedral_angle_3_deg 11.664 r_sphericity_free 9.944 r_dihedral_angle_1_deg 6.984 r_sphericity_bonded 6.211 r_scangle_it 5.815 r_scbond_it 4.038 r_mcangle_it 3.135 r_rigid_bond_restr 2.271 r_mcbond_it 2.097 r_angle_refined_deg 1.09 r_chiral_restr 0.099 r_gen_planes_refined 0.012 r_bond_refined_d 0.007 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 932 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling