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Monomeric Griffithsin in Complex with a High-Mannose Branched Carbohydrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LKY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1 M mixture of imidazole, sodium cacodylate, MES, and bis-tris, 0.1 M mixture of L-Na-glutamate, alanine, glycine, lysine-HCl, and serine, 30% w/v PEG MME 550 and PEG 20000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.22 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.5 α = 90 b = 90.5 β = 90 c = 27.8 γ = 90
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 2009-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 0.97 50 99.8 0.055 14.8 4.8 66935
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) 0.97 1 98.4 0.507 2 3.4 6566
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 (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 3LKY 0.97 30 66889 65888 1001 99.74 0.144 0.143 0.151 0.155 0.1601 RANDOM 15.233
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 -0.02 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.641 r_dihedral_angle_4_deg 15.749 r_dihedral_angle_3_deg 10.569 r_dihedral_angle_1_deg 7.435 r_sphericity_bonded 7.147 r_scangle_it 5.048 r_scbond_it 4.018 r_mcangle_it 2.809 r_angle_other_deg 2.6 r_angle_refined_deg 2.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.641 r_dihedral_angle_4_deg 15.749 r_dihedral_angle_3_deg 10.569 r_dihedral_angle_1_deg 7.435 r_sphericity_bonded 7.147 r_scangle_it 5.048 r_scbond_it 4.018 r_mcangle_it 2.809 r_angle_other_deg 2.6 r_angle_refined_deg 2.579 r_rigid_bond_restr 2.413 r_mcbond_other 2.317 r_mcbond_it 2.224 r_chiral_restr 0.299 r_symmetry_vdw_other 0.241 r_nbd_other 0.231 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.21 r_nbtor_refined 0.184 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.155 r_nbtor_other 0.123 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.009 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 902 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 122
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling