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Monomeric Griffithsin with a Single Gly-Ser Insertion and Mutations to Remove Residual Self-Association
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 3.5 298 0.1M citric acid, 3M NaCl, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.17 43.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.4 α = 90 b = 55.4 β = 90 c = 61.8 γ = 120
Symmetry Space Group P 31 2 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 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 99.9 0.082 13.3 7.1 65427
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 99.4 0.78 2 5.2 6418
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 65253 976 99.95 0.152 0.152 0.1588 0.165 0.1707 RANDOM 14.177
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] -0.32 -0.16 -0.32 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.359 r_dihedral_angle_4_deg 20.308 r_dihedral_angle_3_deg 12.457 r_dihedral_angle_1_deg 7.898 r_sphericity_bonded 4.818 r_scangle_it 4.704 r_scbond_it 3.707 r_mcangle_it 2.669 r_angle_refined_deg 2.304 r_mcbond_it 2.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.359 r_dihedral_angle_4_deg 20.308 r_dihedral_angle_3_deg 12.457 r_dihedral_angle_1_deg 7.898 r_sphericity_bonded 4.818 r_scangle_it 4.704 r_scbond_it 3.707 r_mcangle_it 2.669 r_angle_refined_deg 2.304 r_mcbond_it 2.165 r_rigid_bond_restr 1.814 r_mcbond_other 1.358 r_angle_other_deg 1.322 r_symmetry_vdw_other 0.327 r_symmetry_hbond_refined 0.273 r_xyhbond_nbd_refined 0.254 r_symmetry_vdw_refined 0.242 r_nbd_other 0.212 r_nbd_refined 0.209 r_nbtor_refined 0.19 r_chiral_restr 0.133 r_nbtor_other 0.105 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 888 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 1
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