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Crystal structure of a complex of griffithsin with mannose at 0.94 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GTY PDB ENTRY 2GTY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 1.8M magnesium sulfate,0.1M MES, 1:10 ratio of griffithsin monomers to mannose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.38 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.74 α = 90 b = 39.44 β = 91 c = 57.16 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 MARMOSAIC 300 mm CCD 2006-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.7 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 0.94 50 95.5 0.064 3.4 148669 148669 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 0.94 0.96 75
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2GTY 0.94 30 148669 148646 1498 95.17 0.1355 0.1355 0.1355 0.1453 0.15607 0.1553 RANDOM 8.641
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] -0.5 -0.35 -0.14 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.7 r_dihedral_angle_4_deg 17.269 r_dihedral_angle_3_deg 12.48 r_sphericity_free 11.393 r_dihedral_angle_1_deg 7.342 r_sphericity_bonded 6.485 r_angle_other_deg 4.862 r_scangle_it 4.273 r_scbond_it 3.645 r_mcangle_it 2.418
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.7 r_dihedral_angle_4_deg 17.269 r_dihedral_angle_3_deg 12.48 r_sphericity_free 11.393 r_dihedral_angle_1_deg 7.342 r_sphericity_bonded 6.485 r_angle_other_deg 4.862 r_scangle_it 4.273 r_scbond_it 3.645 r_mcangle_it 2.418 r_angle_refined_deg 2.154 r_mcbond_it 1.945 r_rigid_bond_restr 1.838 r_mcbond_other 1.13 r_nbd_refined 0.293 r_symmetry_vdw_refined 0.271 r_symmetry_vdw_other 0.263 r_nbd_other 0.231 r_xyhbond_nbd_refined 0.202 r_nbtor_refined 0.199 r_symmetry_hbond_refined 0.191 r_nbtor_other 0.164 r_chiral_restr 0.152 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1888 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction DENZO data reduction HKL-2000 data scaling SCALEPACK data scaling PHASER phasing