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Crystal structure of a designed Cyanovirin-N homolog lectin; LKAMG in P21 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M5M PSEUDO-MONOMERIC CV-N (1M5M)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 277 40 mg/ml protein in 0.2 M Li2SO4, 0.1 M Tris-HCl (pH 8.5), and 30% PEG 4000 at 8 to 1 ratio between protein and mother liquor, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.11 41.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.876 α = 90 b = 34.444 β = 101.24 c = 45.632 γ = 90
Symmetry Space Group P 1 21 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 CCD RIGAKU SATURN 944 MIRRORS 2006-10-16 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 1.56 24.49 95.5 0.047 19.9 3.9 14212 2
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) 1.56 1.62 71.4 0.175 3.2 2.21
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 PSEUDO-MONOMERIC CV-N (1M5M) 1.56 24.49 12776 1436 95.5 0.187 0.183 0.1798 0.225 0.2214 RANDOM 17.88
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] -0.53 -0.14 -0.18 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.281 r_dihedral_angle_4_deg 21.919 r_dihedral_angle_3_deg 11.102 r_dihedral_angle_1_deg 7.624 r_scangle_it 5.965 r_scbond_it 3.696 r_mcangle_it 2.311 r_mcbond_it 1.375 r_angle_refined_deg 1.141 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.281 r_dihedral_angle_4_deg 21.919 r_dihedral_angle_3_deg 11.102 r_dihedral_angle_1_deg 7.624 r_scangle_it 5.965 r_scbond_it 3.696 r_mcangle_it 2.311 r_mcbond_it 1.375 r_angle_refined_deg 1.141 r_chiral_restr 0.098 r_gen_planes_refined 0.013 r_bond_refined_d 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 863 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling